[inst/site/create_table.R:19:58:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/create_table.R#L19) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  dp_selection = filter(data_df, V3 == sample(indexes, 1) ),
                                                         ^
```
[inst/site/create_table.R:21:62:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/create_table.R#L21) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    "select * from taxonomy where V3 == ", sample(indexes, 1) )), times = 100
                                                             ^
```
[inst/site/merge_and_plot_bwa_assignments.R:12:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_bwa_assignments.R#L12) *style:* **Variable or function name should be snake_case.**
```r
srcFile <- args[1]
^~~~~~~
```
[inst/site/merge_and_plot_bwa_assignments.R:13:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_bwa_assignments.R#L13) *style:* **Variable or function name should be snake_case.**
```r
destFile <- args[2]
^~~~~~~~
```
[inst/site/merge_and_plot_bwa_assignments.R:14:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_bwa_assignments.R#L14) *style:* **Variable or function name should be snake_case.**
```r
taxonomyLevelArg <- args[3]
^~~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_bwa_assignments.R:15:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_bwa_assignments.R#L15) *style:* **Variable or function name should be snake_case.**
```r
plotTitleArg <- args[4]
^~~~~~~~~~~~
```
[inst/site/merge_and_plot_bwa_assignments.R:16:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_bwa_assignments.R#L16) *style:* **Variable or function name should be snake_case.**
```r
plotFileArg <- args[5]
^~~~~~~~~~~
```
[inst/site/merge_and_plot_bwa_assignments.R:21:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_bwa_assignments.R#L21) *style:* **Variable or function name should be snake_case.**
```r
  rowLimitArg <- args[6]
  ^~~~~~~~~~~
```
[inst/site/merge_and_plot_bwa_assignments.R:22:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_bwa_assignments.R#L22) *style:* **Variable or function name should be snake_case.**
```r
  sortingOrderArg <- args[7]
  ^~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_bwa_assignments.R:24:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_bwa_assignments.R#L24) *style:* **Variable or function name should be snake_case.**
```r
  rowLimitArg <- 60
  ^~~~~~~~~~~
```
[inst/site/merge_and_plot_bwa_assignments.R:25:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_bwa_assignments.R#L25) *style:* **Variable or function name should be snake_case.**
```r
  sortingOrderArg <- "abundance"
  ^~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_diamond_assignments.R:12:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_diamond_assignments.R#L12) *style:* **Variable or function name should be snake_case.**
```r
srcFile <- args[1]
^~~~~~~
```
[inst/site/merge_and_plot_diamond_assignments.R:13:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_diamond_assignments.R#L13) *style:* **Variable or function name should be snake_case.**
```r
destFile <- args[2]
^~~~~~~~
```
[inst/site/merge_and_plot_diamond_assignments.R:14:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_diamond_assignments.R#L14) *style:* **Variable or function name should be snake_case.**
```r
taxonomyLevelArg <- args[3]
^~~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_diamond_assignments.R:15:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_diamond_assignments.R#L15) *style:* **Variable or function name should be snake_case.**
```r
plotTitleArg <- args[4]
^~~~~~~~~~~~
```
[inst/site/merge_and_plot_diamond_assignments.R:16:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_diamond_assignments.R#L16) *style:* **Variable or function name should be snake_case.**
```r
plotFileArg <- args[5]
^~~~~~~~~~~
```
[inst/site/merge_and_plot_diamond_assignments.R:21:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_diamond_assignments.R#L21) *style:* **Variable or function name should be snake_case.**
```r
  rowLimitArg <- args[6]
  ^~~~~~~~~~~
```
[inst/site/merge_and_plot_diamond_assignments.R:22:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_diamond_assignments.R#L22) *style:* **Variable or function name should be snake_case.**
```r
  sortingOrderArg <- args[7]
  ^~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_diamond_assignments.R:24:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_diamond_assignments.R#L24) *style:* **Variable or function name should be snake_case.**
```r
  rowLimitArg <- 60
  ^~~~~~~~~~~
```
[inst/site/merge_and_plot_diamond_assignments.R:25:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_diamond_assignments.R#L25) *style:* **Variable or function name should be snake_case.**
```r
  sortingOrderArg <- "abundance"
  ^~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_edge_assignments.R:12:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_edge_assignments.R#L12) *style:* **Variable or function name should be snake_case.**
```r
srcFile <- args[1]
^~~~~~~
```
[inst/site/merge_and_plot_edge_assignments.R:13:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_edge_assignments.R#L13) *style:* **Variable or function name should be snake_case.**
```r
destFile <- args[2]
^~~~~~~~
```
[inst/site/merge_and_plot_edge_assignments.R:14:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_edge_assignments.R#L14) *style:* **Variable or function name should be snake_case.**
```r
taxonomyLevelArg <- args[3]
^~~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_edge_assignments.R:15:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_edge_assignments.R#L15) *style:* **Variable or function name should be snake_case.**
```r
plotTitleArg <- args[4]
^~~~~~~~~~~~
```
[inst/site/merge_and_plot_edge_assignments.R:16:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_edge_assignments.R#L16) *style:* **Variable or function name should be snake_case.**
```r
plotFileArg <- args[5]
^~~~~~~~~~~
```
[inst/site/merge_and_plot_edge_assignments.R:17:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_edge_assignments.R#L17) *style:* **Variable or function name should be snake_case.**
```r
assignerType <- args[6]
^~~~~~~~~~~~
```
[inst/site/merge_and_plot_edge_assignments.R:22:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_edge_assignments.R#L22) *style:* **Variable or function name should be snake_case.**
```r
  rowLimitArg <- args[7]
  ^~~~~~~~~~~
```
[inst/site/merge_and_plot_edge_assignments.R:23:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_edge_assignments.R#L23) *style:* **Variable or function name should be snake_case.**
```r
  sortingOrderArg <- args[8]
  ^~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_edge_assignments.R:25:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_edge_assignments.R#L25) *style:* **Variable or function name should be snake_case.**
```r
  rowLimitArg <- 60
  ^~~~~~~~~~~
```
[inst/site/merge_and_plot_edge_assignments.R:26:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_edge_assignments.R#L26) *style:* **Variable or function name should be snake_case.**
```r
  sortingOrderArg <- "abundance"
  ^~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_gottcha_assignments.R:12:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_gottcha_assignments.R#L12) *style:* **Variable or function name should be snake_case.**
```r
srcFile <- args[1]
^~~~~~~
```
[inst/site/merge_and_plot_gottcha_assignments.R:13:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_gottcha_assignments.R#L13) *style:* **Variable or function name should be snake_case.**
```r
destFile <- args[2]
^~~~~~~~
```
[inst/site/merge_and_plot_gottcha_assignments.R:14:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_gottcha_assignments.R#L14) *style:* **Variable or function name should be snake_case.**
```r
taxonomyLevelArg <- args[3]
^~~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_gottcha_assignments.R:15:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_gottcha_assignments.R#L15) *style:* **Variable or function name should be snake_case.**
```r
plotTitleArg <- args[4]
^~~~~~~~~~~~
```
[inst/site/merge_and_plot_gottcha_assignments.R:16:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_gottcha_assignments.R#L16) *style:* **Variable or function name should be snake_case.**
```r
plotFileArg <- args[5]
^~~~~~~~~~~
```
[inst/site/merge_and_plot_gottcha_assignments.R:21:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_gottcha_assignments.R#L21) *style:* **Variable or function name should be snake_case.**
```r
  rowLimitArg <- args[6]
  ^~~~~~~~~~~
```
[inst/site/merge_and_plot_gottcha_assignments.R:22:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_gottcha_assignments.R#L22) *style:* **Variable or function name should be snake_case.**
```r
  sortingOrderArg <- args[7]
  ^~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_gottcha_assignments.R:24:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_gottcha_assignments.R#L24) *style:* **Variable or function name should be snake_case.**
```r
  rowLimitArg <- 60
  ^~~~~~~~~~~
```
[inst/site/merge_and_plot_gottcha_assignments.R:25:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_gottcha_assignments.R#L25) *style:* **Variable or function name should be snake_case.**
```r
  sortingOrderArg <- "abundance"
  ^~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_gottcha2_assignments.R:12:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_gottcha2_assignments.R#L12) *style:* **Variable or function name should be snake_case.**
```r
srcFile <- args[1]
^~~~~~~
```
[inst/site/merge_and_plot_gottcha2_assignments.R:13:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_gottcha2_assignments.R#L13) *style:* **Variable or function name should be snake_case.**
```r
destFile <- args[2]
^~~~~~~~
```
[inst/site/merge_and_plot_gottcha2_assignments.R:14:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_gottcha2_assignments.R#L14) *style:* **Variable or function name should be snake_case.**
```r
taxonomyLevelArg <- args[3]
^~~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_gottcha2_assignments.R:15:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_gottcha2_assignments.R#L15) *style:* **Variable or function name should be snake_case.**
```r
plotTitleArg <- args[4]
^~~~~~~~~~~~
```
[inst/site/merge_and_plot_gottcha2_assignments.R:16:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_gottcha2_assignments.R#L16) *style:* **Variable or function name should be snake_case.**
```r
plotFileArg <- args[5]
^~~~~~~~~~~
```
[inst/site/merge_and_plot_gottcha2_assignments.R:21:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_gottcha2_assignments.R#L21) *style:* **Variable or function name should be snake_case.**
```r
  rowLimitArg <- args[6]
  ^~~~~~~~~~~
```
[inst/site/merge_and_plot_gottcha2_assignments.R:22:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_gottcha2_assignments.R#L22) *style:* **Variable or function name should be snake_case.**
```r
  sortingOrderArg <- args[7]
  ^~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_gottcha2_assignments.R:24:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_gottcha2_assignments.R#L24) *style:* **Variable or function name should be snake_case.**
```r
  rowLimitArg <- 60
  ^~~~~~~~~~~
```
[inst/site/merge_and_plot_gottcha2_assignments.R:25:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_gottcha2_assignments.R#L25) *style:* **Variable or function name should be snake_case.**
```r
  sortingOrderArg <- "abundance"
  ^~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_kraken_assignments.R:12:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_kraken_assignments.R#L12) *style:* **Variable or function name should be snake_case.**
```r
srcFile <- args[1]
^~~~~~~
```
[inst/site/merge_and_plot_kraken_assignments.R:13:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_kraken_assignments.R#L13) *style:* **Variable or function name should be snake_case.**
```r
destFile <- args[2]
^~~~~~~~
```
[inst/site/merge_and_plot_kraken_assignments.R:14:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_kraken_assignments.R#L14) *style:* **Variable or function name should be snake_case.**
```r
taxonomyLevelArg <- args[3]
^~~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_kraken_assignments.R:15:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_kraken_assignments.R#L15) *style:* **Variable or function name should be snake_case.**
```r
plotTitleArg <- args[4]
^~~~~~~~~~~~
```
[inst/site/merge_and_plot_kraken_assignments.R:16:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_kraken_assignments.R#L16) *style:* **Variable or function name should be snake_case.**
```r
plotFileArg <- args[5]
^~~~~~~~~~~
```
[inst/site/merge_and_plot_kraken_assignments.R:21:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_kraken_assignments.R#L21) *style:* **Variable or function name should be snake_case.**
```r
  rowLimitArg <- args[6]
  ^~~~~~~~~~~
```
[inst/site/merge_and_plot_kraken_assignments.R:22:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_kraken_assignments.R#L22) *style:* **Variable or function name should be snake_case.**
```r
  sortingOrderArg <- args[7]
  ^~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_kraken_assignments.R:24:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_kraken_assignments.R#L24) *style:* **Variable or function name should be snake_case.**
```r
  rowLimitArg <- 60
  ^~~~~~~~~~~
```
[inst/site/merge_and_plot_kraken_assignments.R:25:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_kraken_assignments.R#L25) *style:* **Variable or function name should be snake_case.**
```r
  sortingOrderArg <- "abundance"
  ^~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_kraken_assignments.R:29:69:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_kraken_assignments.R#L29) *style:* **Put spaces around all infix operators.**
```r
merged <- merge_edge_assignments(load_edge_assignments(srcFile, type= "kraken"))
                                                                   ~^
```
[inst/site/merge_and_plot_metaphlan_assignments.R:12:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_metaphlan_assignments.R#L12) *style:* **Variable or function name should be snake_case.**
```r
srcFile <- args[1]
^~~~~~~
```
[inst/site/merge_and_plot_metaphlan_assignments.R:13:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_metaphlan_assignments.R#L13) *style:* **Variable or function name should be snake_case.**
```r
destFile <- args[2]
^~~~~~~~
```
[inst/site/merge_and_plot_metaphlan_assignments.R:14:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_metaphlan_assignments.R#L14) *style:* **Variable or function name should be snake_case.**
```r
taxonomyLevelArg <- args[3]
^~~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_metaphlan_assignments.R:15:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_metaphlan_assignments.R#L15) *style:* **Variable or function name should be snake_case.**
```r
plotTitleArg <- args[4]
^~~~~~~~~~~~
```
[inst/site/merge_and_plot_metaphlan_assignments.R:16:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_metaphlan_assignments.R#L16) *style:* **Variable or function name should be snake_case.**
```r
plotFileArg <- args[5]
^~~~~~~~~~~
```
[inst/site/merge_and_plot_metaphlan_assignments.R:21:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_metaphlan_assignments.R#L21) *style:* **Variable or function name should be snake_case.**
```r
  rowLimitArg <- args[6]
  ^~~~~~~~~~~
```
[inst/site/merge_and_plot_metaphlan_assignments.R:22:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_metaphlan_assignments.R#L22) *style:* **Variable or function name should be snake_case.**
```r
  sortingOrderArg <- args[7]
  ^~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_metaphlan_assignments.R:24:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_metaphlan_assignments.R#L24) *style:* **Variable or function name should be snake_case.**
```r
  rowLimitArg <- 60
  ^~~~~~~~~~~
```
[inst/site/merge_and_plot_metaphlan_assignments.R:25:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_metaphlan_assignments.R#L25) *style:* **Variable or function name should be snake_case.**
```r
  sortingOrderArg <- "abundance"
  ^~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_pangia_assignments.R:12:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_pangia_assignments.R#L12) *style:* **Variable or function name should be snake_case.**
```r
srcFile <- args[1]
^~~~~~~
```
[inst/site/merge_and_plot_pangia_assignments.R:13:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_pangia_assignments.R#L13) *style:* **Variable or function name should be snake_case.**
```r
destFile <- args[2]
^~~~~~~~
```
[inst/site/merge_and_plot_pangia_assignments.R:14:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_pangia_assignments.R#L14) *style:* **Variable or function name should be snake_case.**
```r
taxonomyLevelArg <- args[3]
^~~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_pangia_assignments.R:15:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_pangia_assignments.R#L15) *style:* **Variable or function name should be snake_case.**
```r
plotTitleArg <- args[4]
^~~~~~~~~~~~
```
[inst/site/merge_and_plot_pangia_assignments.R:16:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_pangia_assignments.R#L16) *style:* **Variable or function name should be snake_case.**
```r
plotFileArg <- args[5]
^~~~~~~~~~~
```
[inst/site/merge_and_plot_pangia_assignments.R:21:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_pangia_assignments.R#L21) *style:* **Variable or function name should be snake_case.**
```r
  rowLimitArg <- args[6]
  ^~~~~~~~~~~
```
[inst/site/merge_and_plot_pangia_assignments.R:22:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_pangia_assignments.R#L22) *style:* **Variable or function name should be snake_case.**
```r
  sortingOrderArg <- args[7]
  ^~~~~~~~~~~~~~~
```
[inst/site/merge_and_plot_pangia_assignments.R:24:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_pangia_assignments.R#L24) *style:* **Variable or function name should be snake_case.**
```r
  rowLimitArg <- 60
  ^~~~~~~~~~~
```
[inst/site/merge_and_plot_pangia_assignments.R:25:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_and_plot_pangia_assignments.R#L25) *style:* **Variable or function name should be snake_case.**
```r
  sortingOrderArg <- "abundance"
  ^~~~~~~~~~~~~~~
```
[inst/site/merge_gottcha_assignments.R:11:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_gottcha_assignments.R#L11) *style:* **Variable or function name should be snake_case.**
```r
srcFile <- args[1]
^~~~~~~
```
[inst/site/merge_gottcha_assignments.R:14:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/inst/site/merge_gottcha_assignments.R#L14) *style:* **Variable or function name should be snake_case.**
```r
destFile <- args[2]
^~~~~~~~
```
[R/load_edge_assignment.R:33:13:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L33) *style:* **Variable or function name should be snake_case.**
```r
  levels <- TAXA <- LEVEL <- COUNT <- ABUNDANCE <- NULL
            ^~~~
```
[R/load_edge_assignment.R:33:21:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L33) *style:* **Variable or function name should be snake_case.**
```r
  levels <- TAXA <- LEVEL <- COUNT <- ABUNDANCE <- NULL
                    ^~~~~
```
[R/load_edge_assignment.R:33:30:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L33) *style:* **Variable or function name should be snake_case.**
```r
  levels <- TAXA <- LEVEL <- COUNT <- ABUNDANCE <- NULL
                             ^~~~~
```
[R/load_edge_assignment.R:33:30:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L33) *warning:* **local variable ‘COUNT’ assigned but may not be used**
```r
  levels <- TAXA <- LEVEL <- COUNT <- ABUNDANCE <- NULL
                             ^~~~~
```
[R/load_edge_assignment.R:33:39:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L33) *style:* **Variable or function name should be snake_case.**
```r
  levels <- TAXA <- LEVEL <- COUNT <- ABUNDANCE <- NULL
                                      ^~~~~~~~~
```
[R/load_edge_assignment.R:34:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L34) *style:* **Variable or function name should be snake_case.**
```r
  ROLLUP <- NAME <- ASSIGN <- REL_ABU <- READ_COUNT <- NULL
  ^~~~~~
```
[R/load_edge_assignment.R:34:13:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L34) *style:* **Variable or function name should be snake_case.**
```r
  ROLLUP <- NAME <- ASSIGN <- REL_ABU <- READ_COUNT <- NULL
            ^~~~
```
[R/load_edge_assignment.R:34:21:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L34) *style:* **Variable or function name should be snake_case.**
```r
  ROLLUP <- NAME <- ASSIGN <- REL_ABU <- READ_COUNT <- NULL
                    ^~~~~~
```
[R/load_edge_assignment.R:34:31:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L34) *style:* **Variable or function name should be snake_case.**
```r
  ROLLUP <- NAME <- ASSIGN <- REL_ABU <- READ_COUNT <- NULL
                              ^~~~~~~
```
[R/load_edge_assignment.R:34:42:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L34) *style:* **Variable or function name should be snake_case.**
```r
  ROLLUP <- NAME <- ASSIGN <- REL_ABU <- READ_COUNT <- NULL
                                         ^~~~~~~~~~
```
[R/load_edge_assignment.R:35:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L35) *style:* **Variable or function name should be snake_case.**
```r
  REL_ABUNDANCE <- NORM_COV <- READ_COUNT_RNR <- ASSIGNED <- NULL
  ^~~~~~~~~~~~~
```
[R/load_edge_assignment.R:35:20:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L35) *style:* **Variable or function name should be snake_case.**
```r
  REL_ABUNDANCE <- NORM_COV <- READ_COUNT_RNR <- ASSIGNED <- NULL
                   ^~~~~~~~
```
[R/load_edge_assignment.R:35:32:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L35) *style:* **Variable or function name should be snake_case.**
```r
  REL_ABUNDANCE <- NORM_COV <- READ_COUNT_RNR <- ASSIGNED <- NULL
                               ^~~~~~~~~~~~~~
```
[R/load_edge_assignment.R:35:50:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L35) *style:* **Variable or function name should be snake_case.**
```r
  REL_ABUNDANCE <- NORM_COV <- READ_COUNT_RNR <- ASSIGNED <- NULL
                                                 ^~~~~~~~
```
[R/load_edge_assignment.R:38:7:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L38) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( !file.exists(filepath) ) {
      ^
```
[R/load_edge_assignment.R:38:30:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L38) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( !file.exists(filepath) ) {
                             ^
```
[R/load_edge_assignment.R:44:7:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L44) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( 0 == file_info$size ) {
      ^
```
[R/load_edge_assignment.R:44:27:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L44) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( 0 == file_info$size ) {
                          ^
```
[R/load_edge_assignment.R:45:16:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L45) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    data.frame( LEVEL = character(), TAXA = character(), COUNT = integer(), ABUNDANCE = double())
               ^
```
[R/load_edge_assignment.R:54:9:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L54) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( 'bwa' == type ){
        ^
```
[R/load_edge_assignment.R:54:23:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L54) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( 'bwa' == type ){
                      ^
```
[R/load_edge_assignment.R:56:32:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L56) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      if (0 == length(df$LEVEL) ) {
                               ^
```
[R/load_edge_assignment.R:57:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L57) *style:* **Lines should not be more than 100 characters.**
```r
        data.frame( LEVEL = character(), TAXA = character(), COUNT = integer(), ABUNDANCE = double())
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/load_edge_assignment.R:57:20:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L57) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        data.frame( LEVEL = character(), TAXA = character(), COUNT = integer(), ABUNDANCE = double())
                   ^
```
[R/load_edge_assignment.R:61:56:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L61) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
        levels <- plyr::ddply(df, "LEVEL", function(x) { sum(x$ROLLUP) })
                                                       ^
```
[R/load_edge_assignment.R:64:12:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L64) *style:* **Variable or function name should be snake_case.**
```r
        df$ABUNDANCE <- df$ROLLUP / df$SUM * 100
           ^~~~~~~~~
```
[R/load_edge_assignment.R:67:23:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L67) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
        as.data.frame( dplyr::select(df, LEVEL, TAXA, COUNT = ROLLUP, ABUNDANCE))
                      ^
```
[R/load_edge_assignment.R:69:16:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L69) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    } else if ( 'diamond' == type ){
               ^
```
[R/load_edge_assignment.R:69:34:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L69) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    } else if ( 'diamond' == type ){
                                 ^
```
[R/load_edge_assignment.R:70:21:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L70) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      as.data.frame( dplyr::select(df, LEVEL, TAXA = NAME, COUNT = ASSIGN, ABUNDANCE = REL_ABU))
                    ^
```
[R/load_edge_assignment.R:71:16:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L71) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    } else if ( 'gottcha2' == type ){
               ^
```
[R/load_edge_assignment.R:71:35:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L71) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    } else if ( 'gottcha2' == type ){
                                  ^
```
[R/load_edge_assignment.R:72:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L72) *style:* **Lines should not be more than 100 characters.**
```r
      as.data.frame( dplyr::select(df, LEVEL, TAXA = NAME, COUNT = READ_COUNT, ABUNDANCE = REL_ABUNDANCE))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/load_edge_assignment.R:72:21:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L72) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      as.data.frame( dplyr::select(df, LEVEL, TAXA = NAME, COUNT = READ_COUNT, ABUNDANCE = REL_ABUNDANCE))
                    ^
```
[R/load_edge_assignment.R:73:16:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L73) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    } else if ( 'gottcha' == type ){
               ^
```
[R/load_edge_assignment.R:73:34:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L73) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    } else if ( 'gottcha' == type ){
                                 ^
```
[R/load_edge_assignment.R:74:21:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L74) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      as.data.frame( dplyr::select(df, LEVEL, TAXA, COUNT = READ_COUNT, ABUNDANCE = NORM_COV))
                    ^
```
[R/load_edge_assignment.R:75:16:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L75) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    } else if ( 'kraken' == type ){
               ^
```
[R/load_edge_assignment.R:75:33:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L75) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    } else if ( 'kraken' == type ){
                                ^
```
[R/load_edge_assignment.R:78:10:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L78) *style:* **Variable or function name should be snake_case.**
```r
      df$ABUNDANCE <- df$ROLLUP / max_rollup * 100
         ^~~~~~~~~
```
[R/load_edge_assignment.R:79:21:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L79) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      as.data.frame( dplyr::select(df, LEVEL, TAXA, COUNT = ROLLUP, ABUNDANCE))
                    ^
```
[R/load_edge_assignment.R:80:16:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L80) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    } else if ( 'metaphlan' == type ){
               ^
```
[R/load_edge_assignment.R:80:36:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L80) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    } else if ( 'metaphlan' == type ){
                                   ^
```
[R/load_edge_assignment.R:81:21:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L81) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      as.data.frame( dplyr::select(df, LEVEL, TAXA, COUNT = ASSIGNED, ABUNDANCE = ROLLUP))
                    ^
```
[R/load_edge_assignment.R:82:16:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L82) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    } else if ( 'pangia' == type ){
               ^
```
[R/load_edge_assignment.R:82:33:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L82) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    } else if ( 'pangia' == type ){
                                ^
```
[R/load_edge_assignment.R:83:10:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L83) *style:* **Variable or function name should be snake_case.**
```r
      df$READ_COUNT_RNR = as.integer(df$READ_COUNT_RNR)
         ^~~~~~~~~~~~~~
```
[R/load_edge_assignment.R:83:25:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L83) *style:* **Use <-, not =, for assignment.**
```r
      df$READ_COUNT_RNR = as.integer(df$READ_COUNT_RNR)
                        ^
```
[R/load_edge_assignment.R:84:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L84) *style:* **Lines should not be more than 100 characters.**
```r
      as.data.frame( dplyr::select(df, LEVEL, TAXA = NAME, COUNT = READ_COUNT_RNR, ABUNDANCE = REL_ABUNDANCE))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/load_edge_assignment.R:84:21:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L84) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      as.data.frame( dplyr::select(df, LEVEL, TAXA = NAME, COUNT = READ_COUNT_RNR, ABUNDANCE = REL_ABUNDANCE))
                    ^
```
[R/load_edge_assignment.R:86:18:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L86) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
      data.frame( LEVEL = character(), TAXA = character(), COUNT = integer(), ABUNDANCE = double())
                 ^
```
[R/load_edge_assignment.R:90:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L90) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/load_edge_assignment.R:91:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignment.R#L91) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[R/load_edge_assignments.R:35:7:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignments.R#L35) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( !file.exists(filepath) ) {
      ^
```
[R/load_edge_assignments.R:35:30:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignments.R#L35) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( !file.exists(filepath) ) {
                             ^
```
[R/load_edge_assignments.R:44:7:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignments.R#L44) *style:* **Use <-, not =, for assignment.**
```r
  res = list()
      ^
```
[R/load_edge_assignments.R:46:16:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignments.R#L46) *style:* **Use <-, not =, for assignment.**
```r
    cur_asgnmt = load_edge_assignment(df[prj_name == df$V1, ]$V2, type)
               ^
```
[R/load_edge_assignments.R:46:18:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignments.R#L46) *warning:* **no visible global function definition for ‘load_edge_assignment’**
```r
    cur_asgnmt = load_edge_assignment(df[prj_name == df$V1, ]$V2, type)
                 ^~~~~~~~~~~~~~~~~~~~
```
[R/load_edge_assignments.R:47:9:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/load_edge_assignments.R#L47) *style:* **Use <-, not =, for assignment.**
```r
    res = c(res, list(cur_asgnmt))
        ^
```
[R/merge_edge_assignments.R:32:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/merge_edge_assignments.R#L32) *style:* **Variable or function name should be snake_case.**
```r
  LEVEL <- TAXA <- ABUNDANCE <- NULL # fix the CRAN note
  ^~~~~
```
[R/merge_edge_assignments.R:32:12:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/merge_edge_assignments.R#L32) *style:* **Variable or function name should be snake_case.**
```r
  LEVEL <- TAXA <- ABUNDANCE <- NULL # fix the CRAN note
           ^~~~
```
[R/merge_edge_assignments.R:32:20:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/merge_edge_assignments.R#L32) *style:* **Variable or function name should be snake_case.**
```r
  LEVEL <- TAXA <- ABUNDANCE <- NULL # fix the CRAN note
                   ^~~~~~~~~
```
[R/merge_edge_counts.R:19:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/merge_edge_counts.R#L19) *style:* **Variable or function name should be snake_case.**
```r
  LEVEL <- TAXA <- COUNT <- NULL # fix the CRAN note
  ^~~~~
```
[R/merge_edge_counts.R:19:12:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/merge_edge_counts.R#L19) *style:* **Variable or function name should be snake_case.**
```r
  LEVEL <- TAXA <- COUNT <- NULL # fix the CRAN note
           ^~~~
```
[R/merge_edge_counts.R:19:20:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/merge_edge_counts.R#L19) *style:* **Variable or function name should be snake_case.**
```r
  LEVEL <- TAXA <- COUNT <- NULL # fix the CRAN note
                   ^~~~~
```
[R/plot_edge_assignment.R:28:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/plot_edge_assignment.R#L28) *style:* **Variable or function name should be snake_case.**
```r
  LEVEL <- TAXA <- ABUNDANCE <- tool <- NULL # fix the CRAN note
  ^~~~~
```
[R/plot_edge_assignment.R:28:12:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/plot_edge_assignment.R#L28) *style:* **Variable or function name should be snake_case.**
```r
  LEVEL <- TAXA <- ABUNDANCE <- tool <- NULL # fix the CRAN note
           ^~~~
```
[R/plot_edge_assignment.R:28:20:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/plot_edge_assignment.R#L28) *style:* **Variable or function name should be snake_case.**
```r
  LEVEL <- TAXA <- ABUNDANCE <- tool <- NULL # fix the CRAN note
                   ^~~~~~~~~
```
[R/plot_edge_assignment.R:40:8:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/plot_edge_assignment.R#L40) *style:* **Variable or function name should be snake_case.**
```r
  vals$ABUNDANCE <- vals$ABUNDANCE
       ^~~~~~~~~
```
[R/plot_edge_assignment.R:43:8:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/plot_edge_assignment.R#L43) *style:* **Variable or function name should be snake_case.**
```r
  vals$TAXA <- factor(x = vals$TAXA, levels = vals$TAXA, ordered = T)
       ^~~~
```
[R/plot_edge_assignment.R:48:27:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/plot_edge_assignment.R#L48) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
     p <- ggplot2::ggplot( data = vals, ggplot2::aes(y = TAXA, x = tool, fill = ABUNDANCE) ) +
                          ^
```
[R/plot_edge_assignment.R:48:91:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/plot_edge_assignment.R#L48) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
     p <- ggplot2::ggplot( data = vals, ggplot2::aes(y = TAXA, x = tool, fill = ABUNDANCE) ) +
                                                                                ^
```
[R/plot_merged_assignment.R:38:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/plot_merged_assignment.R#L38) *style:* **Lines should not be more than 100 characters.**
```r
#'                                        "HMP side-to-side", file.path(tempdir(), "assignment.pdf"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_merged_assignment.R:45:3:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/plot_merged_assignment.R#L45) *style:* **Variable or function name should be snake_case.**
```r
  TAXA <- LEVEL <- SUM <- value <- variable <- NULL # fix the CRAN note
  ^~~~
```
[R/plot_merged_assignment.R:45:11:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/plot_merged_assignment.R#L45) *style:* **Variable or function name should be snake_case.**
```r
  TAXA <- LEVEL <- SUM <- value <- variable <- NULL # fix the CRAN note
          ^~~~~
```
[R/plot_merged_assignment.R:45:20:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/plot_merged_assignment.R#L45) *style:* **Variable or function name should be snake_case.**
```r
  TAXA <- LEVEL <- SUM <- value <- variable <- NULL # fix the CRAN note
                   ^~~
```
[R/plot_merged_assignment.R:105:6:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/plot_merged_assignment.R#L105) *style:* **Variable or function name should be snake_case.**
```r
  df$TAXA <- factor(x = df$TAXA, levels = unique(df$TAXA), ordered = T)
     ^~~~
```
[R/plot_merged_assignment.R:114:71:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/plot_merged_assignment.R#L114) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  column_index <- c(1, project_names_order + 1, as.numeric(dim(df)[2]) )
                                                                      ^
```
[R/plot_merged_assignment.R:116:39:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/plot_merged_assignment.R#L116) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  df <- dplyr::select(df, column_index )
                                      ^
```
[R/plot_merged_assignment.R:125:24:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/plot_merged_assignment.R#L125) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  p <- ggplot2::ggplot( data = melted_df, ggplot2::aes(y = TAXA, x = variable, fill = value) ) +
                       ^
```
[R/plot_merged_assignment.R:125:93:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/plot_merged_assignment.R#L125) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  p <- ggplot2::ggplot( data = melted_df, ggplot2::aes(y = TAXA, x = variable, fill = value) ) +
                                                                                ^
```
[R/plot_merged_assignment.R:164:4:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/plot_merged_assignment.R#L164) *style:* **Commented code should be removed.**
```r
  #p1 <- suppressWarnings(gridExtra::arrangeGrob(p, top = title.grob))
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_merged_assignment.R:171:4:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/plot_merged_assignment.R#L171) *style:* **Commented code should be removed.**
```r
  #suppressWarnings(grid::grid.draw(p1))
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot_merged_assignment.R:180:4:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/R/plot_merged_assignment.R#L180) *style:* **Commented code should be removed.**
```r
  #suppressWarnings(grid::grid.draw(p1))
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_load_bwa_assignment.R:4:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_bwa_assignment.R#L4) *style:* **Lines should not be more than 100 characters.**
```r
dat <- data.frame(load_edge_assignment("../test_data/SSputum-no-RAB/bwa/allReads-bwa.list.txt", type = 'bwa'))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_load_bwa_assignment.R:7:13:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_bwa_assignment.R#L7) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that( dim(dat)[1], equals(558) )
            ^
```
[tests/testthat/test_load_bwa_assignment.R:7:38:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_bwa_assignment.R#L7) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that( dim(dat)[1], equals(558) )
                                     ^
```
[tests/testthat/test_load_bwa_assignment.R:10:13:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_bwa_assignment.R#L10) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that( dim(dat)[2], equals(4) )
            ^
```
[tests/testthat/test_load_bwa_assignment.R:10:36:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_bwa_assignment.R#L10) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that( dim(dat)[2], equals(4) )
                                   ^
```
[tests/testthat/test_load_bwa_assignment.R:13:35:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_bwa_assignment.R#L13) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(colnames(dat), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                  ^
```
[tests/testthat/test_load_bwa_assignment.R:13:76:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_bwa_assignment.R#L13) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(colnames(dat), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                           ^
```
[tests/testthat/test_load_bwa_assignment.R:13:78:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_bwa_assignment.R#L13) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(colnames(dat), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                             ^
```
[tests/testthat/test_load_bwa_assignment.R:18:31:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_bwa_assignment.R#L18) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
family_table <- dplyr::filter( dat, LEVEL == "species")
                              ^
```
[tests/testthat/test_load_bwa_assignment.R:21:26:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_bwa_assignment.R#L21) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
ent_row <- dplyr::filter( family_table, TAXA == "Moraxella catarrhalis")
                         ^
```
[tests/testthat/test_load_bwa_assignment.R:36:40:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_bwa_assignment.R#L36) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                       ^
```
[tests/testthat/test_load_bwa_assignment.R:36:81:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_bwa_assignment.R#L36) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                                ^
```
[tests/testthat/test_load_bwa_assignment.R:36:83:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_bwa_assignment.R#L36) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                                ^
```
[tests/testthat/test_load_bwa_assignment.R:37:40:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_bwa_assignment.R#L37) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(dim(empty_df)[1], equals(0) )
                                       ^
```
[tests/testthat/test_load_bwa_assignment.R:43:40:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_bwa_assignment.R#L43) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                       ^
```
[tests/testthat/test_load_bwa_assignment.R:43:81:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_bwa_assignment.R#L43) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                                ^
```
[tests/testthat/test_load_bwa_assignment.R:43:83:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_bwa_assignment.R#L43) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                                ^
```
[tests/testthat/test_load_bwa_assignment.R:44:40:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_bwa_assignment.R#L44) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(dim(empty_df)[1], equals(0) )
                                       ^
```
[tests/testthat/test_load_diamond_assignment.R:8:13:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_diamond_assignment.R#L8) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that( dim(dat)[1], equals(234) )
            ^
```
[tests/testthat/test_load_diamond_assignment.R:8:38:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_diamond_assignment.R#L8) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that( dim(dat)[1], equals(234) )
                                     ^
```
[tests/testthat/test_load_diamond_assignment.R:11:13:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_diamond_assignment.R#L11) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that( dim(dat)[2], equals(4) )
            ^
```
[tests/testthat/test_load_diamond_assignment.R:11:36:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_diamond_assignment.R#L11) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that( dim(dat)[2], equals(4) )
                                   ^
```
[tests/testthat/test_load_diamond_assignment.R:14:35:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_diamond_assignment.R#L14) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(colnames(dat), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                  ^
```
[tests/testthat/test_load_diamond_assignment.R:14:76:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_diamond_assignment.R#L14) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(colnames(dat), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                           ^
```
[tests/testthat/test_load_diamond_assignment.R:14:78:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_diamond_assignment.R#L14) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(colnames(dat), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                             ^
```
[tests/testthat/test_load_diamond_assignment.R:19:31:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_diamond_assignment.R#L19) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
family_table <- dplyr::filter( dat, LEVEL == "family")
                              ^
```
[tests/testthat/test_load_diamond_assignment.R:23:26:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_diamond_assignment.R#L23) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
ent_row <- dplyr::filter( family_table, TAXA == "Enterobacteriaceae")
                         ^
```
[tests/testthat/test_load_diamond_assignment.R:32:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_diamond_assignment.R#L32) *style:* **Lines should not be more than 100 characters.**
```r
expect_that(load_edge_assignment("../test_data/nonexistentfile.txt", type = 'diamond'), throws_error())
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_load_diamond_assignment.R:38:40:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_diamond_assignment.R#L38) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                       ^
```
[tests/testthat/test_load_diamond_assignment.R:38:81:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_diamond_assignment.R#L38) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                                ^
```
[tests/testthat/test_load_diamond_assignment.R:38:83:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_diamond_assignment.R#L38) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
                                                                                ^
```
[tests/testthat/test_load_diamond_assignment.R:39:40:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_diamond_assignment.R#L39) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that(dim(empty_df)[1], equals(0) )
                                       ^
```
[tests/testthat/test_load_diamond_assignments.R:21:1:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_diamond_assignments.R#L21) *style:* **Lines should not be more than 100 characters.**
```r
expect_that(load_edge_assignments("../test_data/nonexistentfile.txt", type = 'diamond'), throws_error())
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test_load_gottcha_assignment.R:8:13:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_gottcha_assignment.R#L8) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that( dim(dat)[1], equals(65) )
            ^
```
[tests/testthat/test_load_gottcha_assignment.R:8:37:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_gottcha_assignment.R#L8) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that( dim(dat)[1], equals(65) )
                                    ^
```
[tests/testthat/test_load_gottcha_assignment.R:11:13:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_gottcha_assignment.R#L11) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that( dim(dat)[2], equals(4) )
            ^
```
[tests/testthat/test_load_gottcha_assignment.R:11:36:](https://github.com/seninp-bioinfo/MetaComp/blob/35f0d2afb17a65020644b296e2a2f3012981d79c/tests/testthat/test_load_gottcha_assignment.R#L11) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
expect_that( dim(dat)[2], equals(4) )


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-27-den-pantheon-ci-project.pantheonsite.io/)

Created multidev environment [ci-27](https://dashboard.pantheon.io/sites/87c029d1-419a-4431-86a2-376625d9be3f#ci-27) for den-pantheon-ci-project.


It's okay.


On a side note - we should either update all JS to use ES6 variable declarations (`let`/`const`) or stick with `var` in all places ;)


Created multidev environment [graywolf#ci-596](https://dashboard.pantheon.io/sites/4bf71429-83ad-4601-9cbc-b5e5b1b1c7a7#ci-596).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-596-graywolf.pantheonsite.io/)


Quick web-based example using queue's to allow people to add drawings to the list!


Hey Aaron! Make sure in future to .gitignore your dist folder as well as your node_modules!


Looks Fine


Hey, this looks great.  I was working on a similar project for one of the carrier variants but haven't gotten quite as far as you have.

I have a couple of questions/requests:
Would you mind splitting the s5pv210-aries.dts file into two - one specific to the i9000 and another that can be used for any of the carrier variants?  This is what has been done for the SGS3 and Note2.  I can do this if you want.  Or, they can be kept separate if you prefer
Do you mind me putting pull requests against your branch or should I maintain my own trees?  My variant needs an additional patch for the onenand to work properly (https://github.com/xc-racer99/linux/commit/9d2f8bdaf039908f8ac7112fe41920df17b19684)
Are you intending to mainline your work?  I noticed you've submitted a couple of fixes upstream.  However, it appears you're still using the exynos4210 version of FIMD
Does your SD card (sdhci2) work with the common s5pv210 pinctrl?  I needed to adjust the pull and the drivestrength or else I would get errors when reading/writing data despite everything being probed correctly

Also, FYI, it is possible to chainload u-boot from the stock Samsung bootloader.  You could probably use my tree at https://github.com/xc-racer99/u-boot-galaxys4g without changes, but note that it wouldn't have SDHCI0 enabled as that's not present on my variant (probably just need to copy that bit from goni).  Serial console works through the USB port.

Thanks!


I can only second that! Thank you @LeMinaw!


This commit broke CI: https://travis-ci.org/freeorion/freeorion/jobs/393307216


Commit the changes


Created multidev environment [wilder#pr-af-prela](https://dashboard.pantheon.io/sites/14808007-3d80-488e-b078-193b788aa4a3#pr-af-prela).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-af-prela-wilder.pantheonsite.io/)


бессмысленно здесь присваивать значение локальной переменной
достаточно последней строчкой написать `find_station(name)`
это и будет возвращать метод


Also your gitignore file needs to be at the root of the project, not nested inside another folder. Come see me and we can remove these node modules which you don't really want to push up.


см. выше


Created multidev environment [wilder#ci-559](https://dashboard.pantheon.io/sites/14808007-3d80-488e-b078-193b788aa4a3#ci-559).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-559-wilder.pantheonsite.io/)


The following doc(s) have been deployed to the [3685dnsdo](https://3685dnsdo-static-docs.pantheonsite.io/docs) Multidev environment:
- [/docs/dns](https://3685dnsdo-static-docs.pantheonsite.io/docs/dns)


Perfecto, los cambios funcionaron 👍


You should change these names to be anonymous. Same with `vg_names` below.


Планируется в следующий раз дописать методы:
```
public void transformImage(ActionEvent actionEvent) { ... }
public void antitransformImage(ActionEvent actionEvent) { ... }
```
`transformImage` — для применения **DFT** к загруженному изображению
`antitransformImage` — для применения **iDFT** к загруженному изображению

**DFT** (Discrete Fourier Transform) — дискретное преобразование Фурье
**iDFT** (Inverse Discrete Fourier Transform) — обратное дискретное преобразование Фурье


Created multidev environment [composer-digital-initiatives#ci-394](https://dashboard.pantheon.io/sites/3d35643a-2d94-44d8-ac78-4f1526e12dcf#ci-394).

[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://ci-394-composer-digital-initiatives.pantheonsite.io/)


не очень верно здесь использовать инстанс-переменную
инстанс-переменные обычно используются для хранения значений, а у тебя здесь просто нужно вернуть результат и все, дальше уже не нужна переменная
по хорошему здесь вообще не нужно ничего присваивать, просто написать последней строкой `gets.chomp`
а там, где вызываешь использовать локальную пременную
вместо:
```ruby
    choose_train
    train = find_train(@number)
```
написать:
```ruby
    number = choose_train
    train = find_train(number)
```
или даже:
```ruby
    train = find_train(choose_train)
```


Sample comment