[R/pheatmap-internal.R:1:1:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/pheatmap-internal.R#L1) *style:* **Variable or function name should be snake_case.**
```r
.emptyPheatmapAnnotations <- list(
^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pheatmap-internal.R:10:1:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/pheatmap-internal.R#L10) *style:* **Variable or function name should be snake_case.**
```r
.pheatmapAnnotations <- function(
^~~~~~~~~~~~~~~~~~~~
```
[R/pheatmap-internal.R:13:5:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/pheatmap-internal.R#L13) *style:* **Variable or function name should be snake_case.**
```r
    legendColor
    ^~~~~~~~~~~
```
[R/pheatmap-internal.R:16:5:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/pheatmap-internal.R#L16) *warning:* **no visible global function definition for ‘assert_is_character’**
```r
    assert_is_character(blacklist)
    ^~~~~~~~~~~~~~~~~~~
```
[R/pheatmap-internal.R:17:5:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/pheatmap-internal.R#L17) *warning:* **no visible global function definition for ‘assertIsHexColorFunctionOrNULL’**
```r
    assertIsHexColorFunctionOrNULL(legendColor)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pheatmap-internal.R:20:13:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/pheatmap-internal.R#L20) *warning:* **no visible global function definition for ‘colData’**
```r
    data <- colData(object)
            ^~~~~~~
```
[R/pheatmap-internal.R:21:5:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/pheatmap-internal.R#L21) *style:* **Variable or function name should be snake_case.**
```r
    interestingGroups <- interestingGroups(object)
    ^~~~~~~~~~~~~~~~~
```
[R/pheatmap-internal.R:29:16:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/pheatmap-internal.R#L29) *warning:* **no visible binding for global variable ‘.emptyPheatmapAnnotations’**
```r
        return(.emptyPheatmapAnnotations)
               ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pheatmap-internal.R:32:5:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/pheatmap-internal.R#L32) *warning:* **no visible global function definition for ‘assertHasRownames’**
```r
    assertHasRownames(data)
    ^~~~~~~~~~~~~~~~~
```
[R/pheatmap-internal.R:51:5:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/pheatmap-internal.R#L51) *style:* **Variable or function name should be snake_case.**
```r
    hasLevels <- vapply(
    ^~~~~~~~~
```
[R/pheatmap-internal.R:61:16:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/pheatmap-internal.R#L61) *warning:* **no visible binding for global variable ‘.emptyPheatmapAnnotations’**
```r
        return(.emptyPheatmapAnnotations)  # nocov
               ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pheatmap-internal.R:74:17:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/pheatmap-internal.R#L74) *warning:* **no visible global function definition for ‘assert_is_factor’**
```r
                assert_is_factor(x)
                ^~~~~~~~~~~~~~~~
```
[R/pheatmap-internal.R:96:1:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/pheatmap-internal.R#L96) *style:* **Variable or function name should be snake_case.**
```r
.pheatmapArgs <- function(args) {
^~~~~~~~~~~~~
```
[R/pheatmap-internal.R:97:5:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/pheatmap-internal.R#L97) *warning:* **no visible global function definition for ‘assert_is_list’**
```r
    assert_is_list(args)
    ^~~~~~~~~~~~~~
```
[R/pheatmap-internal.R:98:5:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/pheatmap-internal.R#L98) *warning:* **no visible global function definition for ‘assert_has_names’**
```r
    assert_has_names(args)
    ^~~~~~~~~~~~~~~~
```
[R/pheatmap-internal.R:100:5:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/pheatmap-internal.R#L100) *style:* **Variable or function name should be snake_case.**
```r
    invalidNames <- grep("[._]", names(args), value = TRUE)
    ^~~~~~~~~~~~
```
[R/pheatmap-internal.R:107:20:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/pheatmap-internal.R#L107) *warning:* **no visible global function definition for ‘snake’, Did you mean 'save'?**
```r
    names(args) <- snake(names(args))
                   ^~~~~
```
[R/pheatmap-internal.R:108:5:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/pheatmap-internal.R#L108) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
    assert_is_subset(names(args), formalArgs(pheatmap))
    ^~~~~~~~~~~~~~~~
```
[R/pheatmap-internal.R:108:46:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/pheatmap-internal.R#L108) *warning:* **no visible binding for global variable ‘pheatmap’, Did you mean 'heatmap'?**
```r
    assert_is_subset(names(args), formalArgs(pheatmap))
                                             ^~~~~~~~
```
[R/pheatmap-internal.R:109:5:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/pheatmap-internal.R#L109) *warning:* **no visible global function definition for ‘assert_has_no_duplicates’**
```r
    assert_has_no_duplicates(names(args))
    ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pheatmap-internal.R:116:1:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/pheatmap-internal.R#L116) *style:* **Variable or function name should be snake_case.**
```r
.pheatmapColorPalette <- function(color = NULL, n = 256L) {
^~~~~~~~~~~~~~~~~~~~~
```
[R/pheatmap-internal.R:120:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/pheatmap-internal.R#L120) *warning:* **no visible global function definition for ‘assert_all_are_hex_colors’**
```r
        assert_all_are_hex_colors(color)
        ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pheatmap-internal.R:125:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/pheatmap-internal.R#L125) *warning:* **no visible global function definition for ‘assertIsHexColorFunctionOrNULL’**
```r
        assertIsHexColorFunctionOrNULL(color)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pheatmap-internal.R:129:30:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/pheatmap-internal.R#L129) *warning:* **no visible global function definition for ‘brewer.pal’**
```r
        colorRampPalette(rev(brewer.pal(n = 7L, name = "RdYlBu")))(n)
                             ^~~~~~~~~~
```
[R/plotCountsPerBiotype-methods.R:39:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerBiotype-methods.R#L39) *style:* **Variable or function name should be snake_case.**
```r
        interestingGroups = NULL,
        ^~~~~~~~~~~~~~~~~
```
[R/plotCountsPerBiotype-methods.R:41:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerBiotype-methods.R#L41) *style:* **Variable or function name should be snake_case.**
```r
        countsAxisLabel = "counts"
        ^~~~~~~~~~~~~~~
```
[R/plotCountsPerBiotype-methods.R:44:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerBiotype-methods.R#L44) *warning:* **no visible global function definition for ‘assert_is_scalar’**
```r
        assert_is_scalar(assay)
        ^~~~~~~~~~~~~~~~
```
[R/plotCountsPerBiotype-methods.R:45:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerBiotype-methods.R#L45) *warning:* **no visible global function definition for ‘assertIsAnImplicitInteger’**
```r
        assertIsAnImplicitInteger(n)
        ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotCountsPerBiotype-methods.R:46:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerBiotype-methods.R#L46) *style:* **Variable or function name should be snake_case.**
```r
        interestingGroups <- matchInterestingGroups(
        ^~~~~~~~~~~~~~~~~
```
[R/plotCountsPerBiotype-methods.R:50:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerBiotype-methods.R#L50) *warning:* **no visible global function definition for ‘interestingGroups<-’, Did you mean 'interestingGroups'?**
```r
        interestingGroups(object) <- interestingGroups
        ^~~~~~~~~~~~~~~~~
```
[R/plotCountsPerBiotype-methods.R:51:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerBiotype-methods.R#L51) *warning:* **no visible global function definition for ‘assert_is_a_string’**
```r
        assert_is_a_string(trans)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotCountsPerBiotype-methods.R:52:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerBiotype-methods.R#L52) *warning:* **no visible global function definition for ‘assert_is_a_string’**
```r
        assert_is_a_string(countsAxisLabel)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotCountsPerBiotype-methods.R:54:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerBiotype-methods.R#L54) *style:* **Variable or function name should be snake_case.**
```r
        rowData <- rowData(object)
        ^~~~~~~
```
[R/plotCountsPerBiotype-methods.R:59:13:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerBiotype-methods.R#L59) *style:* **Variable or function name should be snake_case.**
```r
            biotypeCol <- "transcriptBiotype"
            ^~~~~~~~~~
```
[R/plotCountsPerBiotype-methods.R:61:13:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerBiotype-methods.R#L61) *style:* **Variable or function name should be snake_case.**
```r
            biotypeCol <- "geneBiotype"
            ^~~~~~~~~~
```
[R/plotCountsPerBiotype-methods.R:63:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerBiotype-methods.R#L63) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
        assert_is_subset(biotypeCol, colnames(rowData))
        ^~~~~~~~~~~~~~~~
```
[R/plotCountsPerBiotype-methods.R:79:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerBiotype-methods.R#L79) *style:* **Variable or function name should be snake_case.**
```r
        sampleData <- sampleData(object) %>%
        ^~~~~~~~~~
```
[R/plotCountsPerBiotype-methods.R:104:21:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerBiotype-methods.R#L104) *warning:* **no visible global function definition for ‘rename’, Did you mean 'unname'?**
```r
            data <- rename(data, !!sym("sampleID") := !!sym("colname"))
                    ^~~~~~
```
[R/plotCountsPerBiotype-methods.R:104:36:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerBiotype-methods.R#L104) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
            data <- rename(data, !!sym("sampleID") := !!sym("colname"))
                                   ^~~
```
[R/plotCountsPerBiotype-methods.R:104:36:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerBiotype-methods.R#L104) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
            data <- rename(data, !!sym("sampleID") := !!sym("colname"))
                                   ^~~
```
[R/plotCountsPerBiotype-methods.R:104:52:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerBiotype-methods.R#L104) *warning:* **no visible global function definition for ‘:=’, Did you mean ':'?**
```r
            data <- rename(data, !!sym("sampleID") := !!sym("colname"))
                                                   ^~
```
[R/plotCountsPerBiotype-methods.R:180:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerBiotype-methods.R#L180) *style:* **Variable or function name should be snake_case.**
```r
        interestingGroups = NULL,
        ^~~~~~~~~~~~~~~~~
```
[R/plotCountsPerBiotype-methods.R:182:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerBiotype-methods.R#L182) *style:* **Variable or function name should be snake_case.**
```r
        countsAxisLabel = "counts"
        ^~~~~~~~~~~~~~~
```
[R/plotCountsPerBiotype-methods.R:185:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerBiotype-methods.R#L185) *warning:* **no visible global function definition for ‘assert_is_scalar’**
```r
        assert_is_scalar(assay)
        ^~~~~~~~~~~~~~~~
```
[R/plotCountsPerBiotype-methods.R:186:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerBiotype-methods.R#L186) *style:* **Variable or function name should be snake_case.**
```r
        interestingGroups <- matchInterestingGroups(
        ^~~~~~~~~~~~~~~~~
```
[R/plotCountsPerBiotype-methods.R:190:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerBiotype-methods.R#L190) *warning:* **no visible global function definition for ‘interestingGroups<-’, Did you mean 'interestingGroups'?**
```r
        interestingGroups(object) <- interestingGroups
        ^~~~~~~~~~~~~~~~~
```
[R/plotCountsPerBiotype-methods.R:191:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerBiotype-methods.R#L191) *warning:* **no visible global function definition for ‘assert_is_a_string’**
```r
        assert_is_a_string(trans)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotCountsPerBiotype-methods.R:192:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerBiotype-methods.R#L192) *warning:* **no visible global function definition for ‘assert_is_a_string’**
```r
        assert_is_a_string(countsAxisLabel)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotCountsPerBiotype-methods.R:194:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerBiotype-methods.R#L194) *style:* **Variable or function name should be snake_case.**
```r
        rowData <- rowData(object)
        ^~~~~~~
```
[R/plotCountsPerBiotype-methods.R:197:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerBiotype-methods.R#L197) *style:* **Variable or function name should be snake_case.**
```r
        biotypeCol <- "broadClass"
        ^~~~~~~~~~
```
[R/plotCountsPerBiotype-methods.R:198:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerBiotype-methods.R#L198) *warning:* **no visible global function definition for ‘assert_is_subset’**
```r
        assert_is_subset(biotypeCol, colnames(rowData))
        ^~~~~~~~~~~~~~~~
```
[R/plotCountsPerBiotype-methods.R:212:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerBiotype-methods.R#L212) *style:* **Variable or function name should be snake_case.**
```r
        sampleData <- sampleData(object) %>%
        ^~~~~~~~~~
```
[R/plotCountsPerBiotype-methods.R:236:21:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerBiotype-methods.R#L236) *warning:* **no visible global function definition for ‘rename’, Did you mean 'unname'?**
```r
            data <- rename(data, !!sym("sampleID") := !!sym("colname"))
                    ^~~~~~
```
[R/plotCountsPerBiotype-methods.R:236:36:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerBiotype-methods.R#L236) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
            data <- rename(data, !!sym("sampleID") := !!sym("colname"))
                                   ^~~
```
[R/plotCountsPerBiotype-methods.R:236:36:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerBiotype-methods.R#L236) *warning:* **no visible global function definition for ‘sym’, Did you mean 'sum'?**
```r
            data <- rename(data, !!sym("sampleID") := !!sym("colname"))
                                   ^~~
```
[R/plotCountsPerBiotype-methods.R:236:52:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerBiotype-methods.R#L236) *warning:* **no visible global function definition for ‘:=’, Did you mean ':'?**
```r
            data <- rename(data, !!sym("sampleID") := !!sym("colname"))
                                                   ^~
```
[R/plotCountsPerGene-methods.R:31:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerGene-methods.R#L31) *style:* **Variable or function name should be snake_case.**
```r
        interestingGroups = NULL,
        ^~~~~~~~~~~~~~~~~
```
[R/plotCountsPerGene-methods.R:37:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerGene-methods.R#L37) *style:* **Variable or function name should be snake_case.**
```r
        countsAxisLabel = "counts",
        ^~~~~~~~~~~~~~~
```
[R/plotCountsPerGene-methods.R:41:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerGene-methods.R#L41) *warning:* **no visible global function definition for ‘assert_is_scalar’**
```r
        assert_is_scalar(assay)
        ^~~~~~~~~~~~~~~~
```
[R/plotCountsPerGene-methods.R:42:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerGene-methods.R#L42) *style:* **Variable or function name should be snake_case.**
```r
        interestingGroups <- matchInterestingGroups(
        ^~~~~~~~~~~~~~~~~
```
[R/plotCountsPerGene-methods.R:46:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerGene-methods.R#L46) *warning:* **no visible global function definition for ‘interestingGroups<-’, Did you mean 'interestingGroups'?**
```r
        interestingGroups(object) <- interestingGroups
        ^~~~~~~~~~~~~~~~~
```
[R/plotCountsPerGene-methods.R:49:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerGene-methods.R#L49) *warning:* **no visible global function definition for ‘assertIsFillScaleDiscreteOrNULL’**
```r
        assertIsFillScaleDiscreteOrNULL(fill)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotCountsPerGene-methods.R:50:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerGene-methods.R#L50) *warning:* **no visible global function definition for ‘assert_is_a_bool’**
```r
        assert_is_a_bool(flip)
        ^~~~~~~~~~~~~~~~
```
[R/plotCountsPerGene-methods.R:51:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerGene-methods.R#L51) *warning:* **no visible global function definition for ‘assertIsAStringOrNULL’**
```r
        assertIsAStringOrNULL(countsAxisLabel)
        ^~~~~~~~~~~~~~~~~~~~~
```
[R/plotCountsPerGene-methods.R:52:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerGene-methods.R#L52) *warning:* **no visible global function definition for ‘assertIsAStringOrNULL’**
```r
        assertIsAStringOrNULL(title)
        ^~~~~~~~~~~~~~~~~~~~~
```
[R/plotCountsPerGene-methods.R:70:14:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerGene-methods.R#L70) *warning:* **no visible global function definition for ‘ggplot’, Did you mean 'biplot'?**
```r
        p <- ggplot(data = data)
             ^~~~~~
```
[R/plotCountsPerGene-methods.R:124:22:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerGene-methods.R#L124) *warning:* **no visible global function definition for ‘coord_flip’**
```r
            p <- p + coord_flip()
                     ^~~~~~~~~~
```
[R/plotCountsPerGene-methods.R:128:22:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotCountsPerGene-methods.R#L128) *warning:* **no visible global function definition for ‘guides’**
```r
            p <- p + guides(color = FALSE, fill = FALSE)
                     ^~~~~~
```
[R/plotGenderMarkers-methods.R:22:21:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGenderMarkers-methods.R#L22) *warning:* **no visible binding for global variable ‘object’, Did you mean 'objects'?**
```r
        validObject(object)
                    ^~~~~~
```
[R/plotGenderMarkers-methods.R:25:30:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGenderMarkers-methods.R#L25) *warning:* **no visible binding for global variable ‘object’, Did you mean 'objects'?**
```r
        organism <- organism(object)
                             ^~~~~~
```
[R/plotGenderMarkers-methods.R:33:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGenderMarkers-methods.R#L33) *warning:* **no visible global function definition for ‘assert_is_list’**
```r
        assert_is_list(markers)
        ^~~~~~~~~~~~~~
```
[R/plotGenderMarkers-methods.R:36:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGenderMarkers-methods.R#L36) *style:* **Variable or function name should be snake_case.**
```r
        supportedOrganisms <- names(markers) %>%
        ^~~~~~~~~~~~~~~~~~
```
[R/plotGenderMarkers-methods.R:47:29:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGenderMarkers-methods.R#L47) *warning:* **no visible global function definition for ‘camel’, Did you mean 'call'?**
```r
        markers <- markers[[camel(organism)]]
                            ^~~~~
```
[R/plotGenderMarkers-methods.R:48:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGenderMarkers-methods.R#L48) *warning:* **no visible global function definition for ‘assert_is_tbl_df’**
```r
        assert_is_tbl_df(markers)
        ^~~~~~~~~~~~~~~~
```
[R/plotGene-methods.R:41:1:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGene-methods.R#L41) *style:* **Variable or function name should be snake_case.**
```r
.plotGeneFacet <- function(
^~~~~~~~~~~~~~
```
[R/plotGene-methods.R:43:5:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGene-methods.R#L43) *style:* **Variable or function name should be snake_case.**
```r
    countsAxisLabel = "counts",
    ^~~~~~~~~~~~~~~
```
[R/plotGene-methods.R:44:5:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGene-methods.R#L44) *style:* **Variable or function name should be snake_case.**
```r
    medianLine = TRUE,
    ^~~~~~~~~~
```
[R/plotGene-methods.R:48:5:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGene-methods.R#L48) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
    assert_is_all_of(object, "SummarizedExperiment")
    ^~~~~~~~~~~~~~~~
```
[R/plotGene-methods.R:49:5:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGene-methods.R#L49) *style:* **Variable or function name should be snake_case.**
```r
    interestingGroups <- interestingGroups(object)
    ^~~~~~~~~~~~~~~~~
```
[R/plotGene-methods.R:52:13:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGene-methods.R#L52) *warning:* **no visible global function definition for ‘meltCounts’**
```r
    data <- meltCounts(object)
            ^~~~~~~~~~
```
[R/plotGene-methods.R:74:18:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGene-methods.R#L74) *warning:* **no visible binding for global variable ‘.geneMedianLine’**
```r
        p <- p + .geneMedianLine
                 ^~~~~~~~~~~~~~~
```
[R/plotGene-methods.R:82:18:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGene-methods.R#L82) *warning:* **no visible global function definition for ‘guides’**
```r
        p <- p + guides(color = FALSE)
                 ^~~~~~
```
[R/plotGene-methods.R:90:1:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGene-methods.R#L90) *style:* **Variable or function name should be snake_case.**
```r
.plotGeneWide <- function(
^~~~~~~~~~~~~
```
[R/plotGene-methods.R:92:5:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGene-methods.R#L92) *style:* **Variable or function name should be snake_case.**
```r
    countsAxisLabel = "counts",
    ^~~~~~~~~~~~~~~
```
[R/plotGene-methods.R:93:5:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGene-methods.R#L93) *style:* **Variable or function name should be snake_case.**
```r
    medianLine = TRUE,
    ^~~~~~~~~~
```
[R/plotGene-methods.R:97:5:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGene-methods.R#L97) *warning:* **no visible global function definition for ‘assert_is_all_of’**
```r
    assert_is_all_of(object, "SummarizedExperiment")
    ^~~~~~~~~~~~~~~~
```
[R/plotGene-methods.R:98:5:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGene-methods.R#L98) *style:* **Variable or function name should be snake_case.**
```r
    interestingGroups <- interestingGroups(object)
    ^~~~~~~~~~~~~~~~~
```
[R/plotGene-methods.R:101:13:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGene-methods.R#L101) *warning:* **no visible global function definition for ‘meltCounts’**
```r
    data <- meltCounts(object)
            ^~~~~~~~~~
```
[R/plotGene-methods.R:122:18:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGene-methods.R#L122) *warning:* **no visible binding for global variable ‘.geneMedianLine’**
```r
        p <- p + .geneMedianLine
                 ^~~~~~~~~~~~~~~
```
[R/plotGene-methods.R:140:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGene-methods.R#L140) *style:* **Variable or function name should be snake_case.**
```r
        interestingGroups = NULL,
        ^~~~~~~~~~~~~~~~~
```
[R/plotGene-methods.R:141:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGene-methods.R#L141) *style:* **Variable or function name should be snake_case.**
```r
        countsAxisLabel = "counts",
        ^~~~~~~~~~~~~~~
```
[R/plotGene-methods.R:142:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGene-methods.R#L142) *style:* **Variable or function name should be snake_case.**
```r
        medianLine = TRUE,
        ^~~~~~~~~~
```
[R/plotGene-methods.R:149:19:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGene-methods.R#L149) *warning:* **no visible global function definition for ‘as.SummarizedExperiment’**
```r
        object <- as.SummarizedExperiment(object)
                  ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotGene-methods.R:150:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGene-methods.R#L150) *warning:* **no visible global function definition for ‘assert_is_character’**
```r
        assert_is_character(genes)
        ^~~~~~~~~~~~~~~~~~~
```
[R/plotGene-methods.R:152:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGene-methods.R#L152) *warning:* **no visible global function definition for ‘assert_all_are_in_closed_range’**
```r
        assert_all_are_in_closed_range(length(genes), lower = 1L, upper = 20L)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotGene-methods.R:153:18:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGene-methods.R#L153) *warning:* **no visible global function definition for ‘mapGenesToRownames’**
```r
        genes <- mapGenesToRownames(object, genes = genes, strict = FALSE)
                 ^~~~~~~~~~~~~~~~~~
```
[R/plotGene-methods.R:154:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGene-methods.R#L154) *warning:* **no visible global function definition for ‘assert_is_scalar’**
```r
        assert_is_scalar(assay)
        ^~~~~~~~~~~~~~~~
```
[R/plotGene-methods.R:155:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGene-methods.R#L155) *style:* **Variable or function name should be snake_case.**
```r
        interestingGroups <- matchInterestingGroups(
        ^~~~~~~~~~~~~~~~~
```
[R/plotGene-methods.R:159:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGene-methods.R#L159) *warning:* **no visible global function definition for ‘interestingGroups<-’, Did you mean 'interestingGroups'?**
```r
        interestingGroups(object) <- interestingGroups
        ^~~~~~~~~~~~~~~~~
```
[R/plotGene-methods.R:160:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGene-methods.R#L160) *warning:* **no visible global function definition for ‘assert_is_a_bool’**
```r
        assert_is_a_bool(medianLine)
        ^~~~~~~~~~~~~~~~
```
[R/plotGene-methods.R:161:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGene-methods.R#L161) *warning:* **no visible global function definition for ‘assertIsColorScaleDiscreteOrNULL’**
```r
        assertIsColorScaleDiscreteOrNULL(color)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotGene-methods.R:162:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGene-methods.R#L162) *warning:* **no visible global function definition for ‘assert_is_a_bool’**
```r
        assert_is_a_bool(legend)
        ^~~~~~~~~~~~~~~~
```
[R/plotGene-methods.R:166:18:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGene-methods.R#L166) *warning:* **no visible global function definition for ‘assays’, Did you mean 'assay'?**
```r
        assay <- assays(object)[[assay]]
                 ^~~~~~
```
[R/plotGene-methods.R:167:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGene-methods.R#L167) *warning:* **no visible global function definition for ‘assays<-’**
```r
        assays(object) <- list(assay = assay)
        ^~~~~~
```
[R/plotGene-methods.R:172:19:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGene-methods.R#L172) *warning:* **no visible global function definition for ‘convertGenesToSymbols’**
```r
        object <- convertGenesToSymbols(object)
                  ^~~~~~~~~~~~~~~~~~~~~
```
[R/plotGene-methods.R:176:21:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGene-methods.R#L176) *warning:* **no visible binding for global variable ‘.plotGeneFacet’**
```r
            what <- .plotGeneFacet
                    ^~~~~~~~~~~~~~
```
[R/plotGene-methods.R:178:21:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGene-methods.R#L178) *warning:* **no visible binding for global variable ‘.plotGeneWide’**
```r
            what <- .plotGeneWide
                    ^~~~~~~~~~~~~
```
[R/plotGenesDetected-methods.R:24:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGenesDetected-methods.R#L24) *style:* **Variable or function name should be snake_case.**
```r
        interestingGroups = NULL,
        ^~~~~~~~~~~~~~~~~
```
[R/plotGenesDetected-methods.R:26:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGenesDetected-methods.R#L26) *style:* **Variable or function name should be snake_case.**
```r
        minCounts = 1L,
        ^~~~~~~~~
```
[R/plotGenesDetected-methods.R:32:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGenesDetected-methods.R#L32) *warning:* **no visible global function definition for ‘assert_is_scalar’**
```r
        assert_is_scalar(assay)
        ^~~~~~~~~~~~~~~~
```
[R/plotGenesDetected-methods.R:33:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGenesDetected-methods.R#L33) *style:* **Variable or function name should be snake_case.**
```r
        interestingGroups <- matchInterestingGroups(
        ^~~~~~~~~~~~~~~~~
```
[R/plotGenesDetected-methods.R:37:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGenesDetected-methods.R#L37) *warning:* **no visible global function definition for ‘interestingGroups<-’, Did you mean 'interestingGroups'?**
```r
        interestingGroups(object) <- interestingGroups
        ^~~~~~~~~~~~~~~~~
```
[R/plotGenesDetected-methods.R:38:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGenesDetected-methods.R#L38) *warning:* **no visible global function definition for ‘assertIsAnImplicitInteger’**
```r
        assertIsAnImplicitInteger(limit)
        ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotGenesDetected-methods.R:39:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGenesDetected-methods.R#L39) *warning:* **no visible global function definition for ‘assert_all_are_non_negative’**
```r
        assert_all_are_non_negative(limit)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotGenesDetected-methods.R:40:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGenesDetected-methods.R#L40) *warning:* **no visible global function definition for ‘assertIsAnImplicitInteger’**
```r
        assertIsAnImplicitInteger(minCounts)
        ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotGenesDetected-methods.R:41:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGenesDetected-methods.R#L41) *warning:* **no visible global function definition for ‘assert_all_are_in_range’**
```r
        assert_all_are_in_range(minCounts, lower = 1L, upper = Inf)
        ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotGenesDetected-methods.R:42:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGenesDetected-methods.R#L42) *warning:* **no visible global function definition for ‘assert_all_are_non_negative’**
```r
        assert_all_are_non_negative(minCounts)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotGenesDetected-methods.R:43:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGenesDetected-methods.R#L43) *warning:* **no visible global function definition for ‘assertIsFillScaleDiscreteOrNULL’**
```r
        assertIsFillScaleDiscreteOrNULL(fill)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotGenesDetected-methods.R:44:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGenesDetected-methods.R#L44) *warning:* **no visible global function definition for ‘assert_is_a_bool’**
```r
        assert_is_a_bool(flip)
        ^~~~~~~~~~~~~~~~
```
[R/plotGenesDetected-methods.R:45:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGenesDetected-methods.R#L45) *warning:* **no visible global function definition for ‘assertIsAStringOrNULL’**
```r
        assertIsAStringOrNULL(title)
        ^~~~~~~~~~~~~~~~~~~~~
```
[R/plotGenesDetected-methods.R:47:19:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGenesDetected-methods.R#L47) *warning:* **no visible global function definition for ‘assays’, Did you mean 'assay'?**
```r
        counts <- assays(object)[[assay]]
                  ^~~~~~
```
[R/plotGenesDetected-methods.R:52:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGenesDetected-methods.R#L52) *style:* **Variable or function name should be snake_case.**
```r
        geneCount <- colSums(counts >= minCounts)
        ^~~~~~~~~
```
[R/plotGenesDetected-methods.R:78:22:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGenesDetected-methods.R#L78) *warning:* **no visible global function definition for ‘basejump_geom_abline’**
```r
            p <- p + basejump_geom_abline(yintercept = limit)
                     ^~~~~~~~~~~~~~~~~~~~
```
[R/plotGenesDetected-methods.R:86:22:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGenesDetected-methods.R#L86) *warning:* **no visible global function definition for ‘coord_flip’**
```r
            p <- p + coord_flip()
                     ^~~~~~~~~~
```
[R/plotGenesDetected-methods.R:90:22:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotGenesDetected-methods.R#L90) *warning:* **no visible global function definition for ‘guides’**
```r
            p <- p + guides(fill = FALSE)
                     ^~~~~~
```
[R/plotHeatmap-methods.R:115:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L115) *style:* **Variable or function name should be snake_case.**
```r
        interestingGroups = NULL,
        ^~~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:117:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L117) *style:* **Variable or function name should be snake_case.**
```r
        clusterRows = TRUE,
        ^~~~~~~~~~~
```
[R/plotHeatmap-methods.R:118:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L118) *style:* **Variable or function name should be snake_case.**
```r
        clusterCols = TRUE,
        ^~~~~~~~~~~
```
[R/plotHeatmap-methods.R:119:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L119) *style:* **Variable or function name should be snake_case.**
```r
        showRownames = FALSE,
        ^~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:120:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L120) *style:* **Variable or function name should be snake_case.**
```r
        showColnames = TRUE,
        ^~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:121:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L121) *style:* **Variable or function name should be snake_case.**
```r
        treeheightRow = 0L,
        ^~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:122:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L122) *style:* **Variable or function name should be snake_case.**
```r
        treeheightCol = 50L,
        ^~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:124:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L124) *style:* **Variable or function name should be snake_case.**
```r
        legendColor = viridis::viridis,
        ^~~~~~~~~~~
```
[R/plotHeatmap-methods.R:125:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L125) *style:* **Variable or function name should be snake_case.**
```r
        borderColor = NULL,
        ^~~~~~~~~~~
```
[R/plotHeatmap-methods.R:130:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L130) *warning:* **no visible global function definition for ‘assert_all_are_greater_than’**
```r
        assert_all_are_greater_than(nrow(object), 1L)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:131:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L131) *warning:* **no visible global function definition for ‘assert_all_are_greater_than’**
```r
        assert_all_are_greater_than(ncol(object), 1L)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:132:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L132) *warning:* **no visible global function definition for ‘assert_is_scalar’**
```r
        assert_is_scalar(assay)
        ^~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:133:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L133) *style:* **Variable or function name should be snake_case.**
```r
        interestingGroups <- matchInterestingGroups(
        ^~~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:138:13:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L138) *warning:* **no visible global function definition for ‘interestingGroups<-’, Did you mean 'interestingGroups'?**
```r
            interestingGroups(object) <- interestingGroups
            ^~~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:141:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L141) *warning:* **no visible global function definition for ‘assert_is_a_bool’**
```r
        assert_is_a_bool(clusterCols)
        ^~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:142:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L142) *warning:* **no visible global function definition for ‘assert_is_a_bool’**
```r
        assert_is_a_bool(clusterRows)
        ^~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:143:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L143) *warning:* **no visible global function definition for ‘assert_is_a_bool’**
```r
        assert_is_a_bool(showColnames)
        ^~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:144:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L144) *warning:* **no visible global function definition for ‘assert_is_a_bool’**
```r
        assert_is_a_bool(showRownames)
        ^~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:145:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L145) *warning:* **no visible global function definition for ‘assert_is_a_number’**
```r
        assert_is_a_number(treeheightRow)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:146:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L146) *warning:* **no visible global function definition for ‘assert_is_a_number’**
```r
        assert_is_a_number(treeheightCol)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:147:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L147) *warning:* **no visible global function definition for ‘assert_all_are_non_negative’**
```r
        assert_all_are_non_negative(treeheightRow, treeheightCol)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:148:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L148) *warning:* **no visible global function definition for ‘assertIsAStringOrNULL’**
```r
        assertIsAStringOrNULL(borderColor)
        ^~~~~~~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:150:13:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L150) *style:* **Variable or function name should be snake_case.**
```r
            borderColor <- NA
            ^~~~~~~~~~~
```
[R/plotHeatmap-methods.R:152:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L152) *warning:* **no visible global function definition for ‘assertIsAStringOrNULL’**
```r
        assertIsAStringOrNULL(title)
        ^~~~~~~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:158:19:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L158) *warning:* **no visible global function definition for ‘convertGenesToSymbols’**
```r
        object <- convertGenesToSymbols(object)
                  ^~~~~~~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:161:26:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L161) *warning:* **no visible global function definition for ‘assays’, Did you mean 'assay'?**
```r
        mat <- as.matrix(assays(object)[[assay]])
                         ^~~~~~
```
[R/plotHeatmap-methods.R:174:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L174) *warning:* **no visible global function definition for ‘assert_is_list’**
```r
        assert_is_list(x)
        ^~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:179:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L179) *style:* **Variable or function name should be snake_case.**
```r
        annotationCol <- x[["annotationCol"]]
        ^~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:180:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L180) *style:* **Variable or function name should be snake_case.**
```r
        annotationColors <- x[["annotationColors"]]
        ^~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:183:18:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L183) *warning:* **no visible global function definition for ‘.pheatmapColorPalette’**
```r
        color <- .pheatmapColorPalette(color)
                 ^~~~~~~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:186:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L186) *style:* **Variable or function name should be snake_case.**
```r
        sampleNames <- tryCatch(
        ^~~~~~~~~~~
```
[R/plotHeatmap-methods.R:217:17:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L217) *warning:* **no visible global function definition for ‘.pheatmapArgs’**
```r
        args <- .pheatmapArgs(args)
                ^~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:218:24:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L218) *warning:* **no visible binding for global variable ‘pheatmap’, Did you mean 'heatmap'?**
```r
        do.call(what = pheatmap, args = args)
                       ^~~~~~~~
```
[R/plotHeatmap-methods.R:227:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L227) *style:* **Variable or function name should be snake_case.**
```r
        interestingGroups = NULL,
        ^~~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:229:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L229) *style:* **Variable or function name should be snake_case.**
```r
        clusteringMethod = "ward.D2",
        ^~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:230:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L230) *style:* **Variable or function name should be snake_case.**
```r
        showRownames = TRUE,
        ^~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:231:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L231) *style:* **Variable or function name should be snake_case.**
```r
        showColnames = TRUE,
        ^~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:232:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L232) *style:* **Variable or function name should be snake_case.**
```r
        treeheightRow = 0L,
        ^~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:233:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L233) *style:* **Variable or function name should be snake_case.**
```r
        treeheightCol = 50L,
        ^~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:235:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L235) *style:* **Variable or function name should be snake_case.**
```r
        legendColor = viridis::viridis,
        ^~~~~~~~~~~
```
[R/plotHeatmap-methods.R:236:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L236) *style:* **Variable or function name should be snake_case.**
```r
        borderColor = NULL,
        ^~~~~~~~~~~
```
[R/plotHeatmap-methods.R:241:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L241) *warning:* **no visible global function definition for ‘assert_is_scalar’**
```r
        assert_is_scalar(assay)
        ^~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:242:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L242) *warning:* **no visible global function definition for ‘assert_all_are_greater_than’**
```r
        assert_all_are_greater_than(nrow(object), 1L)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:243:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L243) *warning:* **no visible global function definition for ‘assert_all_are_greater_than’**
```r
        assert_all_are_greater_than(ncol(object), 1L)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:244:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L244) *style:* **Variable or function name should be snake_case.**
```r
        interestingGroups <- matchInterestingGroups(
        ^~~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:249:13:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L249) *warning:* **no visible global function definition for ‘interestingGroups<-’, Did you mean 'interestingGroups'?**
```r
            interestingGroups(object) <- interestingGroups
            ^~~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:252:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L252) *warning:* **no visible global function definition for ‘assert_is_a_string’**
```r
        assert_is_a_string(clusteringMethod)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:253:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L253) *warning:* **no visible global function definition for ‘assert_is_a_bool’**
```r
        assert_is_a_bool(showColnames)
        ^~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:254:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L254) *warning:* **no visible global function definition for ‘assert_is_a_bool’**
```r
        assert_is_a_bool(showRownames)
        ^~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:255:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L255) *warning:* **no visible global function definition for ‘assert_is_a_number’**
```r
        assert_is_a_number(treeheightRow)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:256:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L256) *warning:* **no visible global function definition for ‘assert_is_a_number’**
```r
        assert_is_a_number(treeheightCol)
        ^~~~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:257:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L257) *warning:* **no visible global function definition for ‘assert_all_are_non_negative’**
```r
        assert_all_are_non_negative(treeheightRow, treeheightCol)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:258:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L258) *warning:* **no visible global function definition for ‘assertIsAStringOrNULL’**
```r
        assertIsAStringOrNULL(borderColor)
        ^~~~~~~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:260:13:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L260) *style:* **Variable or function name should be snake_case.**
```r
            borderColor <- NA
            ^~~~~~~~~~~
```
[R/plotHeatmap-methods.R:269:26:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L269) *warning:* **no visible global function definition for ‘assays’, Did you mean 'assay'?**
```r
        mat <- as.matrix(assays(object)[[assay]])
                         ^~~~~~
```
[R/plotHeatmap-methods.R:277:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L277) *warning:* **no visible global function definition for ‘assert_is_list’**
```r
        assert_is_list(x)
        ^~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:282:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L282) *style:* **Variable or function name should be snake_case.**
```r
        annotationCol <- x[["annotationCol"]]
        ^~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:283:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L283) *style:* **Variable or function name should be snake_case.**
```r
        annotationColors <- x[["annotationColors"]]
        ^~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:286:18:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L286) *warning:* **no visible global function definition for ‘.pheatmapColorPalette’**
```r
        color <- .pheatmapColorPalette(color)
                 ^~~~~~~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:289:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L289) *style:* **Variable or function name should be snake_case.**
```r
        sampleNames <- tryCatch(
        ^~~~~~~~~~~
```
[R/plotHeatmap-methods.R:321:17:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L321) *warning:* **no visible global function definition for ‘.pheatmapArgs’**
```r
        args <- .pheatmapArgs(args)
                ^~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:326:24:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L326) *warning:* **no visible binding for global variable ‘pheatmap’, Did you mean 'heatmap'?**
```r
        do.call(what = pheatmap, args = args)
                       ^~~~~~~~
```
[R/plotHeatmap-methods.R:331:1:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L331) *style:* **Variable or function name should be snake_case.**
```r
.quantileBreaks <- function(object, n = 10L) {
^~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:332:5:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L332) *warning:* **no visible global function definition for ‘assert_is_matrix’**
```r
    assert_is_matrix(object)
    ^~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:333:5:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L333) *warning:* **no visible global function definition for ‘assert_is_an_integer’**
```r
    assert_is_an_integer(n)
    ^~~~~~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:334:5:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L334) *warning:* **no visible global function definition for ‘assert_all_are_positive’**
```r
    assert_all_are_positive(n)
    ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:345:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L345) *style:* **Variable or function name should be snake_case.**
```r
        interestingGroups = NULL,
        ^~~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:347:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L347) *style:* **Variable or function name should be snake_case.**
```r
        clusterRows = TRUE,
        ^~~~~~~~~~~
```
[R/plotHeatmap-methods.R:348:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L348) *style:* **Variable or function name should be snake_case.**
```r
        clusterCols = TRUE,
        ^~~~~~~~~~~
```
[R/plotHeatmap-methods.R:349:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L349) *style:* **Variable or function name should be snake_case.**
```r
        showRownames = FALSE,
        ^~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:350:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L350) *style:* **Variable or function name should be snake_case.**
```r
        showColnames = TRUE,
        ^~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:351:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L351) *style:* **Variable or function name should be snake_case.**
```r
        treeheightRow = 0L,
        ^~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:352:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L352) *style:* **Variable or function name should be snake_case.**
```r
        treeheightCol = 50L,
        ^~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:354:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L354) *style:* **Variable or function name should be snake_case.**
```r
        legendColor = viridis::viridis,
        ^~~~~~~~~~~
```
[R/plotHeatmap-methods.R:356:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L356) *style:* **Variable or function name should be snake_case.**
```r
        borderColor = NULL,
        ^~~~~~~~~~~
```
[R/plotHeatmap-methods.R:361:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L361) *warning:* **no visible global function definition for ‘assert_all_are_greater_than’**
```r
        assert_all_are_greater_than(nrow(object), 1L)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:362:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L362) *warning:* **no visible global function definition for ‘assert_all_are_greater_than’**
```r
        assert_all_are_greater_than(ncol(object), 1L)
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:363:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L363) *warning:* **no visible global function definition for ‘assert_is_scalar’**
```r
        assert_is_scalar(assay)
        ^~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:364:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L364) *style:* **Variable or function name should be snake_case.**
```r
        interestingGroups <- matchInterestingGroups(
        ^~~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:369:13:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L369) *warning:* **no visible global function definition for ‘interestingGroups<-’, Did you mean 'interestingGroups'?**
```r
            interestingGroups(object) <- interestingGroups
            ^~~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:371:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L371) *warning:* **no visible global function definition for ‘assertIsAnImplicitInteger’**
```r
        assertIsAnImplicitInteger(n)
        ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:373:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L373) *warning:* **no visible global function definition for ‘assert_is_a_bool’**
```r
        assert_is_a_bool(clusterCols)
        ^~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:374:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L374) *warning:* **no visible global function definition for ‘assert_is_a_bool’**
```r
        assert_is_a_bool(clusterRows)
        ^~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:375:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L375) *warning:* **no visible global function definition for ‘assert_is_a_bool’**
```r
        assert_is_a_bool(legend)
        ^~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:376:9:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L376) *warning:* **no visible global function definition for ‘assertIsAStringOrNULL’**
```r
        assertIsAStringOrNULL(borderColor)
        ^~~~~~~~~~~~~~~~~~~~~
```
[R/plotHeatmap-methods.R:378:13:](https://github.com/steinbaugh/basejump.plots/blob/26225e04f3d6a63cb260b486f9487c58e0a350b0/R/plotHeatmap-methods.R#L378) *style:* **Variable or function name should be snake_case.**
```r
            borderColor <- NA
            ^~~~~~~~~~~
```


I quickly scanned it but did not try it yet. I ll definitely look into it.
To my understanding so far assigning a new IP address to a tun/tap device still requires root privileges?!
Also mapping ports on the host network efficiently still requires root privileges (at least to configure iptables using the CNI portmap plugin)?!
Due to these assumptions and since CNI is a common interface but its default plugins require root privileges I am thinking about such a daemon process run by root.
However if it is possible somehow to also assign an IP address to a tun/tap interface as unprivileged user that would be the default solution (as a CNI plugin).
I ll try out slirp4netns...


I have noticed it. The text got lost in commit b3c5fdddca07862960e65a8d02dd952b33cf61d1.


gradle clean build


this is for dsa lab programs


bh


In your table .. what does 1 CPU = physically?

- A kubernetes CPU ==> https://kubernetes.io/docs/concepts/configuration/manage-compute-resources-container/
-  an x86 processor thread?
-  an x86 physical core?


[`1c5e014d48e40eadbf106c2701f86e4adc3274c8`](:ru: )
`Ruby_lang.io`
`.mit`


[tests/testthat/test-lint.R:2:5:](https://github.com/dfjenkins3/singleCellTK/blob/d9a081809cd9a80c3ef95157ae8bbe177e60eba3/tests/testthat/test-lint.R#L2) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(packageVersion("lintr") >= "1.0.2.9000") {
    ^
```


Uppgift 5 och Uppgift 6


There is no distro currently with python lower than 2.6.6 I guess. No probs then


👍 Thanks for incorporating!

Blog post is great!


@njsmith  The recent commit from @mathstuf (See https://github.com/mathstuf/ld64/commit/4eebe0c07e8ab706ed2c54ed718f5083fa0704cd) may help here.

For some context, see https://gitlab.kitware.com/vtk/vtk/issues/17214#note_478688


Läggs till Uppgift 5 och Uppgift 6


Unhandled Failure


Updated in Fedora F27-F30.


Ok, but you're code here will not run as is


Thanks! I will change that.


It seems that `escape()` function is deprecated in JavaScript 1.5 and we should use `encodeURIComponent()` instead.


[R/collapseToString-methods.R:58:9:](https://github.com/steinbaugh/basejump.sanitization/blob/51613e97ead4be0c591c8a3ab1739983e3b51526/R/collapseToString-methods.R#L58) *style:* **Variable or function name should be snake_case.**
```r
        removeNA = FALSE,
        ^~~~~~~~
```
[R/collapseToString-methods.R:116:9:](https://github.com/steinbaugh/basejump.sanitization/blob/51613e97ead4be0c591c8a3ab1739983e3b51526/R/collapseToString-methods.R#L116) *style:* **Variable or function name should be snake_case.**
```r
        removeNA = FALSE,
        ^~~~~~~~
```
[R/makeNames-methods.R:96:1:](https://github.com/steinbaugh/basejump.sanitization/blob/51613e97ead4be0c591c8a3ab1739983e3b51526/R/makeNames-methods.R#L96) *style:* **Variable or function name should be snake_case.**
```r
.sanitizeAcronyms <- function(object) {
^~~~~~~~~~~~~~~~~
```
[R/makeNames-methods.R:119:1:](https://github.com/steinbaugh/basejump.sanitization/blob/51613e97ead4be0c591c8a3ab1739983e3b51526/R/makeNames-methods.R#L119) *style:* **Variable or function name should be snake_case.**
```r
makeNames <- function(names, unique = TRUE) {
^~~~~~~~~
```
[R/makeNames-methods.R:132:1:](https://github.com/steinbaugh/basejump.sanitization/blob/51613e97ead4be0c591c8a3ab1739983e3b51526/R/makeNames-methods.R#L132) *style:* **Variable or function name should be snake_case.**
```r
makeDimnames <- function(object) {
^~~~~~~~~~~~
```
[R/makeNames-methods.R:510:1:](https://github.com/steinbaugh/basejump.sanitization/blob/51613e97ead4be0c591c8a3ab1739983e3b51526/R/makeNames-methods.R#L510) *style:* **Variable or function name should be snake_case.**
```r
camel.list <- camel.atomic
^~~~~~~~~~
```
[R/makeNames-methods.R:522:1:](https://github.com/steinbaugh/basejump.sanitization/blob/51613e97ead4be0c591c8a3ab1739983e3b51526/R/makeNames-methods.R#L522) *style:* **Variable or function name should be snake_case.**
```r
dotted.list <- dotted.atomic
^~~~~~~~~~~
```
[R/makeNames-methods.R:534:1:](https://github.com/steinbaugh/basejump.sanitization/blob/51613e97ead4be0c591c8a3ab1739983e3b51526/R/makeNames-methods.R#L534) *style:* **Variable or function name should be snake_case.**
```r
snake.list <- snake.atomic
^~~~~~~~~~
```
[R/makeNames-methods.R:546:1:](https://github.com/steinbaugh/basejump.sanitization/blob/51613e97ead4be0c591c8a3ab1739983e3b51526/R/makeNames-methods.R#L546) *style:* **Variable or function name should be snake_case.**
```r
upperCamel.list <- upperCamel.atomic
^~~~~~~~~~~~~~~
```
[R/makeNames-methods.R:722:1:](https://github.com/steinbaugh/basejump.sanitization/blob/51613e97ead4be0c591c8a3ab1739983e3b51526/R/makeNames-methods.R#L722) *style:* **Variable or function name should be snake_case.**
```r
camel.data.frame <- camel.matrix
^~~~~~~~~~~~~~~~
```
[R/makeNames-methods.R:734:1:](https://github.com/steinbaugh/basejump.sanitization/blob/51613e97ead4be0c591c8a3ab1739983e3b51526/R/makeNames-methods.R#L734) *style:* **Variable or function name should be snake_case.**
```r
dotted.data.frame <- dotted.matrix
^~~~~~~~~~~~~~~~~
```
[R/makeNames-methods.R:746:1:](https://github.com/steinbaugh/basejump.sanitization/blob/51613e97ead4be0c591c8a3ab1739983e3b51526/R/makeNames-methods.R#L746) *style:* **Variable or function name should be snake_case.**
```r
snake.data.frame <- snake.matrix
^~~~~~~~~~~~~~~~
```
[R/makeNames-methods.R:758:1:](https://github.com/steinbaugh/basejump.sanitization/blob/51613e97ead4be0c591c8a3ab1739983e3b51526/R/makeNames-methods.R#L758) *style:* **Variable or function name should be snake_case.**
```r
upperCamel.data.frame <- upperCamel.matrix
^~~~~~~~~~~~~~~~~~~~~
```
[R/makeNames-methods.R:771:1:](https://github.com/steinbaugh/basejump.sanitization/blob/51613e97ead4be0c591c8a3ab1739983e3b51526/R/makeNames-methods.R#L771) *style:* **Variable or function name should be snake_case.**
```r
camel.DataFrame <- camel.data.frame
^~~~~~~~~~~~~~~
```
[R/makeNames-methods.R:783:1:](https://github.com/steinbaugh/basejump.sanitization/blob/51613e97ead4be0c591c8a3ab1739983e3b51526/R/makeNames-methods.R#L783) *style:* **Variable or function name should be snake_case.**
```r
dotted.DataFrame <- dotted.data.frame
^~~~~~~~~~~~~~~~
```
[R/makeNames-methods.R:795:1:](https://github.com/steinbaugh/basejump.sanitization/blob/51613e97ead4be0c591c8a3ab1739983e3b51526/R/makeNames-methods.R#L795) *style:* **Variable or function name should be snake_case.**
```r
snake.DataFrame <- snake.data.frame
^~~~~~~~~~~~~~~
```
[R/makeNames-methods.R:807:1:](https://github.com/steinbaugh/basejump.sanitization/blob/51613e97ead4be0c591c8a3ab1739983e3b51526/R/makeNames-methods.R#L807) *style:* **Variable or function name should be snake_case.**
```r
upperCamel.DataFrame <- upperCamel.data.frame
^~~~~~~~~~~~~~~~~~~~
```
[R/makeNames-methods.R:903:1:](https://github.com/steinbaugh/basejump.sanitization/blob/51613e97ead4be0c591c8a3ab1739983e3b51526/R/makeNames-methods.R#L903) *style:* **Variable or function name should be snake_case.**
```r
camel.GRangesList <- camel.GRanges
^~~~~~~~~~~~~~~~~
```
[R/makeNames-methods.R:915:1:](https://github.com/steinbaugh/basejump.sanitization/blob/51613e97ead4be0c591c8a3ab1739983e3b51526/R/makeNames-methods.R#L915) *style:* **Variable or function name should be snake_case.**
```r
dotted.GRangesList <- dotted.GRanges
^~~~~~~~~~~~~~~~~~
```
[R/makeNames-methods.R:927:1:](https://github.com/steinbaugh/basejump.sanitization/blob/51613e97ead4be0c591c8a3ab1739983e3b51526/R/makeNames-methods.R#L927) *style:* **Variable or function name should be snake_case.**
```r
snake.GRangesList <- snake.GRanges
^~~~~~~~~~~~~~~~~
```
[R/makeNames-methods.R:939:1:](https://github.com/steinbaugh/basejump.sanitization/blob/51613e97ead4be0c591c8a3ab1739983e3b51526/R/makeNames-methods.R#L939) *style:* **Variable or function name should be snake_case.**
```r
upperCamel.GRangesList <- upperCamel.GRanges
^~~~~~~~~~~~~~~~~~~~~~
```
[R/sanitizeRowData.R:21:1:](https://github.com/steinbaugh/basejump.sanitization/blob/51613e97ead4be0c591c8a3ab1739983e3b51526/R/sanitizeRowData.R#L21) *style:* **Variable or function name should be snake_case.**
```r
sanitizeRowData <- function(object) {
^~~~~~~~~~~~~~~
```
[R/sanitizeSampleData.R:33:1:](https://github.com/steinbaugh/basejump.sanitization/blob/51613e97ead4be0c591c8a3ab1739983e3b51526/R/sanitizeSampleData.R#L33) *style:* **Variable or function name should be snake_case.**
```r
sanitizeSampleData <- function(object) {
^~~~~~~~~~~~~~~~~~
```
[R/sortUnique.R:15:1:](https://github.com/steinbaugh/basejump.sanitization/blob/51613e97ead4be0c591c8a3ab1739983e3b51526/R/sortUnique.R#L15) *style:* **Variable or function name should be snake_case.**
```r
sortUnique <- function(object) {
^~~~~~~~~~
```
[R/toStringUnique.R:13:1:](https://github.com/steinbaugh/basejump.sanitization/blob/51613e97ead4be0c591c8a3ab1739983e3b51526/R/toStringUnique.R#L13) *style:* **Variable or function name should be snake_case.**
```r
toStringUnique <- function(object) {
^~~~~~~~~~~~~~
```
[tests/testthat/test_sanitization.R:6:1:](https://github.com/steinbaugh/basejump.sanitization/blob/51613e97ead4be0c591c8a3ab1739983e3b51526/tests/testthat/test_sanitization.R#L6) *style:* **Variable or function name should be snake_case.**
```r
mpgString <- "18.1, 18.7, 21, 21.4, 22.8"
^~~~~~~~~
```
[tests/testthat/test_sanitization.R:8:1:](https://github.com/steinbaugh/basejump.sanitization/blob/51613e97ead4be0c591c8a3ab1739983e3b51526/tests/testthat/test_sanitization.R#L8) *style:* **Variable or function name should be snake_case.**
```r
DataFrame <- S4Vectors::DataFrame
^~~~~~~~~
```
[tests/testthat/test_sanitization.R:9:1:](https://github.com/steinbaugh/basejump.sanitization/blob/51613e97ead4be0c591c8a3ab1739983e3b51526/tests/testthat/test_sanitization.R#L9) *style:* **Variable or function name should be snake_case.**
```r
hasRownames <- basejump.assertions::hasRownames
^~~~~~~~~~~
```
[tests/testthat/test_sanitization.R:10:1:](https://github.com/steinbaugh/basejump.sanitization/blob/51613e97ead4be0c591c8a3ab1739983e3b51526/tests/testthat/test_sanitization.R#L10) *style:* **Variable or function name should be snake_case.**
```r
rowRanges <- SummarizedExperiment::rowRanges
^~~~~~~~~
```


Wouldn't the proper fix be to have the oldtests target depend on helptags being generated?


@rootfs

As a result of discussion in CSI WG, csi driver needs to bind mount a device to targetPath for block volume.

However, on ```NodeUnpublishVolume```, ```GetDeviceNameFromMount``` doesn't return a proper ```devicePath```.
Because mount command doesn't return ```devicePath```, instead it returns ```devtmpfs``` for block device bind mount case.
As seen in below, ```findmnt``` command seems to return a proper value, so it could be used here.
Are there any good way to call it here inside csi driver code?

```
# touch /tmp/dev
# mount -o bind /dev/rbd0 /tmp/dev
# mount | grep /tmp/dev
devtmpfs on /tmp/dev type devtmpfs (rw,nosuid,seclabel,size=16460544k,nr_inodes=4115136,mode=755)

# findmnt -n -o SOURCE --target /tmp/dev
devtmpfs[/rbd0]
```


[R/graphs.R:239:1:](https://github.com/raubreywhite/fhi/blob/e6f32c4a1934c235ff8f038a072f4860cc785367/R/graphs.R#L239) *style:* **lines should not be more than 120 characters.**
```r
    if (!is.null(dataCIL) & !is.null(dataCIU)) q <- q + stat_stepribbon(aes_string(ymin = dataCIL, ymax = dataCIU), fill = "black", direction = "vh", alpha = 0.4)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:245:1:](https://github.com/raubreywhite/fhi/blob/e6f32c4a1934c235ff8f038a072f4860cc785367/R/graphs.R#L245) *style:* **lines should not be more than 120 characters.**
```r
    if (!is.null(dataCIL) & !is.null(dataCIU)) q <- q + geom_ribbon(aes_string(ymin = dataCIL, ymax = dataCIU), fill = "black", alpha = 0.4)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:252:1:](https://github.com/raubreywhite/fhi/blob/e6f32c4a1934c235ff8f038a072f4860cc785367/R/graphs.R#L252) *style:* **lines should not be more than 120 characters.**
```r
    if (includeMedium | includeHigh) q <- q + geom_point(aes_string(x = "xShifted", y = dataVal), size = 4, fill = "black", data = pd[pd$status %in% c("Medium", "High"), ])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:254:1:](https://github.com/raubreywhite/fhi/blob/e6f32c4a1934c235ff8f038a072f4860cc785367/R/graphs.R#L254) *style:* **lines should not be more than 120 characters.**
```r
  if (includeMedium) q <- q + geom_point(aes_string(x = "xShifted", y = dataVal, colour = shQuote("L2")), size = 2, data = pd[pd$status == "Medium", ])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:255:1:](https://github.com/raubreywhite/fhi/blob/e6f32c4a1934c235ff8f038a072f4860cc785367/R/graphs.R#L255) *style:* **lines should not be more than 120 characters.**
```r
  if (includeHigh) q <- q + geom_point(aes_string(x = "xShifted", y = dataVal, colour = shQuote("L1")), size = 2, data = pd[pd$status == "High", ])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:262:5:](https://github.com/raubreywhite/fhi/blob/e6f32c4a1934c235ff8f038a072f4860cc785367/R/graphs.R#L262) *style:* **Commented code should be removed.**
```r
  # q <- q + scale_xcontinuous("Dato", breaks = breaksDF$xShifted,  labels = breaksDF$printLabel)
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:317:1:](https://github.com/raubreywhite/fhi/blob/e6f32c4a1934c235ff8f038a072f4860cc785367/R/graphs.R#L317) *style:* **lines should not be more than 120 characters.**
```r
  if (includeMedium | includeHigh) q <- q + geom_point(aes_string(y = dataVal), size = 4, fill = "black", data = pd[pd$status %in% c("Medium", "High"), ])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:318:1:](https://github.com/raubreywhite/fhi/blob/e6f32c4a1934c235ff8f038a072f4860cc785367/R/graphs.R#L318) *style:* **lines should not be more than 120 characters.**
```r
  if (includeMedium) q <- q + geom_point(aes_string(y = dataVal, colour = shQuote("L2")), size = 2, data = pd[pd$status == "Medium", ])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:319:1:](https://github.com/raubreywhite/fhi/blob/e6f32c4a1934c235ff8f038a072f4860cc785367/R/graphs.R#L319) *style:* **lines should not be more than 120 characters.**
```r
  if (includeHigh) q <- q + geom_point(aes_string(y = dataVal, colour = shQuote("L1")), size = 2, data = pd[pd$status == "High", ])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:371:1:](https://github.com/raubreywhite/fhi/blob/e6f32c4a1934c235ff8f038a072f4860cc785367/R/graphs.R#L371) *style:* **lines should not be more than 120 characters.**
```r
    q <- q + geom_line(aes_string(y = dataVal, colour = comparisonNames), lwd = 2, alpha = 0.8, data = pd[pd[[highlightCondition]], ])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:375:1:](https://github.com/raubreywhite/fhi/blob/e6f32c4a1934c235ff8f038a072f4860cc785367/R/graphs.R#L375) *style:* **lines should not be more than 120 characters.**
```r
      q <- q + geom_line(aes_string(y = dataVal, colour = shQuote(newName)), lwd = 2, alpha = 0.8, data = pd[pd[[highlightCondition]] & pd[[comparisonNames]] == i, ])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:404:1:](https://github.com/raubreywhite/fhi/blob/e6f32c4a1934c235ff8f038a072f4860cc785367/R/graphs.R#L404) *style:* **lines should not be more than 120 characters.**
```r
MakeLineExcessPlot <- function(pd, x, dataVal, dataZ, dataCIL = NULL, dataCIU = NULL, allPoints = TRUE, title = NULL, pointShift = 0, xShift = 0, weekNumbers = FALSE, step = FALSE, GetCols) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:447:7:](https://github.com/raubreywhite/fhi/blob/e6f32c4a1934c235ff8f038a072f4860cc785367/R/graphs.R#L447) *style:* **Commented code should be removed.**
```r
    # q <- q + stat_stepribbon(aes_string(ymin = L3, ymax = L4, fill = shQuote("L1")), direction="vh", alpha = 0.4)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:448:7:](https://github.com/raubreywhite/fhi/blob/e6f32c4a1934c235ff8f038a072f4860cc785367/R/graphs.R#L448) *style:* **Commented code should be removed.**
```r
    # q <- q + stat_stepribbon(aes_string(ymin = L2, ymax = L3, fill = shQuote("L2")), direction="vh", alpha = 0.4)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:449:7:](https://github.com/raubreywhite/fhi/blob/e6f32c4a1934c235ff8f038a072f4860cc785367/R/graphs.R#L449) *style:* **Commented code should be removed.**
```r
    # q <- q + stat_stepribbon(aes_string(ymin = L1, ymax = L2, fill = shQuote("L3")), direction="vh", alpha = 0.4)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:450:1:](https://github.com/raubreywhite/fhi/blob/e6f32c4a1934c235ff8f038a072f4860cc785367/R/graphs.R#L450) *style:* **lines should not be more than 120 characters.**
```r
    if (!is.null(dataCIL) & !is.null(dataCIU)) q <- q + stat_stepribbon(aes_string(ymin = dataCIL, ymax = dataCIU), fill = "black", direction = "vh", alpha = 0.4)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:453:7:](https://github.com/raubreywhite/fhi/blob/e6f32c4a1934c235ff8f038a072f4860cc785367/R/graphs.R#L453) *style:* **Commented code should be removed.**
```r
    # q <- q + geom_ribbon(aes_string(ymin = L3, ymax = L4, fill = shQuote("L1")), alpha = 0.4)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:454:7:](https://github.com/raubreywhite/fhi/blob/e6f32c4a1934c235ff8f038a072f4860cc785367/R/graphs.R#L454) *style:* **Commented code should be removed.**
```r
    # q <- q + geom_ribbon(aes_string(ymin = L2, ymax = L3, fill = shQuote("L2")), alpha = 0.4)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:455:7:](https://github.com/raubreywhite/fhi/blob/e6f32c4a1934c235ff8f038a072f4860cc785367/R/graphs.R#L455) *style:* **Commented code should be removed.**
```r
    # q <- q + geom_ribbon(aes_string(ymin = L1, ymax = L2, fill = shQuote("L3")), alpha = 0.4)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:456:1:](https://github.com/raubreywhite/fhi/blob/e6f32c4a1934c235ff8f038a072f4860cc785367/R/graphs.R#L456) *style:* **lines should not be more than 120 characters.**
```r
    if (!is.null(dataCIL) & !is.null(dataCIU)) q <- q + geom_ribbon(aes_string(ymin = dataCIL, ymax = dataCIU), fill = "black", alpha = 0.4)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:463:1:](https://github.com/raubreywhite/fhi/blob/e6f32c4a1934c235ff8f038a072f4860cc785367/R/graphs.R#L463) *style:* **lines should not be more than 120 characters.**
```r
    if (includeMedium | includeHigh) q <- q + geom_point(aes_string(x = "xShifted", y = dataVal), size = 4, fill = "black", data = pd[pd$status %in% c("Medium", "High"), ])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:465:1:](https://github.com/raubreywhite/fhi/blob/e6f32c4a1934c235ff8f038a072f4860cc785367/R/graphs.R#L465) *style:* **lines should not be more than 120 characters.**
```r
  if (includeMedium) q <- q + geom_point(aes_string(x = "xShifted", y = dataVal, colour = shQuote("L2")), size = 2, data = pd[pd$status == "Medium", ])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/graphs.R:466:1:](https://github.com/raubreywhite/fhi/blob/e6f32c4a1934c235ff8f038a072f4860cc785367/R/graphs.R#L466) *style:* **lines should not be more than 120 characters.**
```r
  if (includeHigh) q <- q + geom_point(aes_string(x = "xShifted", y = dataVal, colour = shQuote("L1")), size = 2, data = pd[pd$status == "High", ])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/RenderExternally.R:48:5:](https://github.com/raubreywhite/fhi/blob/e6f32c4a1934c235ff8f038a072f4860cc785367/R/RenderExternally.R#L48) *style:* **Commented code should be removed.**
```r
  # file.remove(file.path(tmp_dir,tmp_name))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test.R:6:5:](https://github.com/raubreywhite/fhi/blob/e6f32c4a1934c235ff8f038a072f4860cc785367/tests/testthat/test.R#L6) *style:* **Commented code should be removed.**
```r
  # rmarkdown::render(input=f,output_dir = tempdir())
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


d


@bman8932 Aha! I think the problem is here: Your CSS link is pointing to the washLetter.css that I wrote in class. You want to point that to your file name.


Not unless you want to throw every player in third person whenever someone regenerates...


Thanks! Using this lib for a project. Saved me a lot of time. Asked as a comment on the PR, but that's closed, so I'll take the opportunity to ask @russellballestrini here if we can get this pushed up to PyPi. Will make my dependency management easier :).


Thank you very much for updating!
I was just planning to do that, was pleasantly surprised.


See the method CapabilityRegeneration::get


Yes, I think we can work on the output structure. Personally, I would favor a list containing tracks as rows and columns as properties like track id, event number, trigger number, timestamp, ..., posX/Y (track global/local, hit global/local), chi2, ...
The single or number-of-sensors columns we get already by the branch structure -- for getting one track for one row, we would need to modify the collection in the processor. I guess, or what do you think?


This function filters for genes whose `name` property is `geneSymbol`. However from the JASPAR documentation it looks like this is searchable directly (i.e., instead of `search=geneSymbol`, you can go straight to `name=geneSymbol`).

http://jaspar.genereg.net/api/v1/docs/#matrix-list


~~Why would it do that? I still got the~~
Nvm I missed the ID check


Fix #171


ah okay, so, dumping local_hit and global tracks is not possible? And all four collections (local/global tracks/hits) also not?


Изменилось то, что вместо UPPER используется toupper().
Первое - это самодельный велосипед a_ucc() из utils.h, который принимает только KOI8-R.
Второе - это стандартная функция которая понимает локаль. Первое не будет работать, а второе будет, если компилировать из исходников в кодировке отличной от koi8-r.
Если стоит цель в перспективе компилировать в любой кодировке, то постепенная замена UPPER на toupper - благородное и богоугодное дело. Но даже в этом случае капитализировать нужно всю строку, а не имя в этой строке, потому что это соответствует смыслу совершаемой операции. Иначе если я поменяю формат строки:
"Гадкий %s ловко выбил%s %s%s из ваших рук.\r\n"
У меня будет "Гадкий Сорванец ловко выбил стальной нож из ваших рук."


No wait hold on I did keep it.
Now I'm confused why would it do that?


Added Multi Spread submit from CSV


Do you have plans to fix Django 1.11.x with this patch? If so when will that happen? Thanks.


Oooooo wait you reacted to my comment there

Now I get it.....


[tests/testthat/test-lint.R:2:5:](https://github.com/compbiomed/singleCellTK/blob/431f8ee7a27f74bb2a43e307d9a3eb59bec842bd/tests/testthat/test-lint.R#L2) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(packageVersion("lintr") >= "1.0.2.9000") {
    ^
```


Oh no... here it works again... but... this is now "before" wb branch... so we aren't able to easily merge wb branch into master. Github... grrrrrr.


Successfully aliased the URL <https://simon-kjellberg-pymymovfnv.now.sh> to the following aliases.

* https://simonkjellberg.com
* https://www.simonkjellberg.com
* https://simonkjellberg.se
* https://www.simonkjellberg.se


W taki sposób dodajesz do listy nowy lot. Powinny być dodane dwa (z dwóch części składa się podróż)


The view permission is new in Django 2.1. Django 2.0 and older are not affected.


@tisto agreed, also not a fan of this. And honestly didn't expect this getting merged to `master` like that. But at the same time, I do realize that the herculean Python3 efforts spearheaded by @pbauer depend on some very short time windows where everything passes (until it gets broken again because Py3 isn't tested) and the stars align just right. So at some point the trigger just had to be pulled.

I extracted my analysis of this isolation problem into a separate issue: plone/plone.testing#58 - the steps to reproduce worked (lead to the same test failure initially described) for me this morning. At this point I'm fairly certain that it doesn't have anything to do with either Archetypes, plone.restapi or plone.app.widgets. It just so happens that this specific order is what leads to one way where the isolation issue surfaces.

But during debugging I also was able to reproduce it using the robot tests `plone.app.multilingual` as the first test. In summary, I think it basically affects all `ZSERVER` layer tests, which just happen to be mostly robot tests. I would suggest we continue any discussion in plone/plone.testing#58.