[R/as-points.R:6:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/as-points.R#L6) *style:* **Lines should not be more than 120 characters.**
```r
#' @param input_unit Unit of \code{x}, default is millimeters which is default in \code{ggplot2::geom_text}, among other functions.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/colors.R:23:17:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/colors.R#L23) *style:* **Commas should always have a space after.**
```r
    c('#EF0107','#023474','#9C824A')[1:n]
                ^
```
[R/colors.R:23:27:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/colors.R#L23) *style:* **Commas should always have a space after.**
```r
    c('#EF0107','#023474','#9C824A')[1:n]
                          ^
```
[R/estimate-vaf.R:10:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/estimate-vaf.R#L10) *style:* **Lines should not be more than 120 characters.**
```r
#' @return Object containing expected VAFs if the tumor is on the major (\code{mcn}) or minor allele (\code{lcn}), respectively.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate-vaf.R:17:34:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/estimate-vaf.R#L17) *style:* **Put spaces around all infix operators.**
```r
    tumor_normal_alleles = purity*tcn + (1-purity)*2 # total number of alleles in sample
                                ~^~
```
[R/estimate-vaf.R:17:43:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/estimate-vaf.R#L17) *style:* **Put spaces around all infix operators.**
```r
    tumor_normal_alleles = purity*tcn + (1-purity)*2 # total number of alleles in sample
                                         ~^~
```
[R/estimate-vaf.R:17:51:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/estimate-vaf.R#L17) *style:* **Put spaces around all infix operators.**
```r
    tumor_normal_alleles = purity*tcn + (1-purity)*2 # total number of alleles in sample
                                                 ~^~
```
[R/estimate-vaf.R:19:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/estimate-vaf.R#L19) *style:* **Lines should not be more than 120 characters.**
```r
    mcn_mut_alleles = (purity*mcn + (1-purity)) # number of mutated alleles in tumor if mcn, plus mut alleles in normal cells
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate-vaf.R:19:30:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/estimate-vaf.R#L19) *style:* **Put spaces around all infix operators.**
```r
    mcn_mut_alleles = (purity*mcn + (1-purity)) # number of mutated alleles in tumor if mcn, plus mut alleles in normal cells
                            ~^~
```
[R/estimate-vaf.R:19:39:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/estimate-vaf.R#L19) *style:* **Put spaces around all infix operators.**
```r
    mcn_mut_alleles = (purity*mcn + (1-purity)) # number of mutated alleles in tumor if mcn, plus mut alleles in normal cells
                                     ~^~
```
[R/estimate-vaf.R:20:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/estimate-vaf.R#L20) *style:* **Lines should not be more than 120 characters.**
```r
    lcn_mut_alleles = (purity*lcn + (1-purity)) # number of mutated alleles in tumor if lcn, plus mut alleles in normal cells
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate-vaf.R:20:30:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/estimate-vaf.R#L20) *style:* **Put spaces around all infix operators.**
```r
    lcn_mut_alleles = (purity*lcn + (1-purity)) # number of mutated alleles in tumor if lcn, plus mut alleles in normal cells
                            ~^~
```
[R/estimate-vaf.R:20:39:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/estimate-vaf.R#L20) *style:* **Put spaces around all infix operators.**
```r
    lcn_mut_alleles = (purity*lcn + (1-purity)) # number of mutated alleles in tumor if lcn, plus mut alleles in normal cells
                                     ~^~
```
[R/estimate-vaf.R:22:32:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/estimate-vaf.R#L22) *style:* **Put spaces around all infix operators.**
```r
    c(vaf_mcn = mcn_mut_alleles/tumor_normal_alleles, vaf_lcn = lcn_mut_alleles/tumor_normal_alleles)
                              ~^~
```
[R/estimate-vaf.R:22:80:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/estimate-vaf.R#L22) *style:* **Put spaces around all infix operators.**
```r
    c(vaf_mcn = mcn_mut_alleles/tumor_normal_alleles, vaf_lcn = lcn_mut_alleles/tumor_normal_alleles)
                                                                              ~^~
```
[R/estimate-vaf.R:30:34:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/estimate-vaf.R#L30) *style:* **Put spaces around all infix operators.**
```r
    tumor_normal_alleles = purity*tcn + (1-purity)*2 # total number of alleles in sample
                                ~^~
```
[R/estimate-vaf.R:30:43:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/estimate-vaf.R#L30) *style:* **Put spaces around all infix operators.**
```r
    tumor_normal_alleles = purity*tcn + (1-purity)*2 # total number of alleles in sample
                                         ~^~
```
[R/estimate-vaf.R:30:51:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/estimate-vaf.R#L30) *style:* **Put spaces around all infix operators.**
```r
    tumor_normal_alleles = purity*tcn + (1-purity)*2 # total number of alleles in sample
                                                 ~^~
```
[R/estimate-vaf.R:32:29:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/estimate-vaf.R#L32) *style:* **Put spaces around all infix operators.**
```r
    mcn_mut_alleles = purity*mcn # number of mutated alleles in tumor if mcn, plus mut alleles in normal cells
                           ~^~
```
[R/estimate-vaf.R:33:29:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/estimate-vaf.R#L33) *style:* **Put spaces around all infix operators.**
```r
    lcn_mut_alleles = purity*lcn # number of mutated alleles in tumor if lcn, plus mut alleles in normal cells
                           ~^~
```
[R/estimate-vaf.R:35:32:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/estimate-vaf.R#L35) *style:* **Put spaces around all infix operators.**
```r
    c(vaf_mcn = mcn_mut_alleles/tumor_normal_alleles, vaf_lcn = lcn_mut_alleles/tumor_normal_alleles)
                              ~^~
```
[R/estimate-vaf.R:35:80:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/estimate-vaf.R#L35) *style:* **Put spaces around all infix operators.**
```r
    c(vaf_mcn = mcn_mut_alleles/tumor_normal_alleles, vaf_lcn = lcn_mut_alleles/tumor_normal_alleles)
                                                                              ~^~
```
[R/facets-closeup.R:37:18:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/facets-closeup.R#L37) *style:* **Variable or function name should be snake_case.**
```r
        fit$cncf$cnlr.median = fit$cncf$cnlr.median - out$dipLogR
                 ^~~~~~~~~~~
```
[R/ggplot2-themes.R:40:34:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/ggplot2-themes.R#L40) *style:* **Commas should always have a space after.**
```r
        plot.margin = unit(c(0.5,0.5,0.5,0.5), 'lines')
                                 ^
```
[R/ggplot2-themes.R:40:38:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/ggplot2-themes.R#L40) *style:* **Commas should always have a space after.**
```r
        plot.margin = unit(c(0.5,0.5,0.5,0.5), 'lines')
                                     ^
```
[R/ggplot2-themes.R:40:42:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/ggplot2-themes.R#L40) *style:* **Commas should always have a space after.**
```r
        plot.margin = unit(c(0.5,0.5,0.5,0.5), 'lines')
                                         ^
```
[R/ggplot2-themes.R:49:39:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/ggplot2-themes.R#L49) *style:* **Put spaces around all infix operators.**
```r
        line = element_line(size = .75*(.75/1.6), lineend = 'round'),
                                     ~^~
```
[R/ggplot2-themes.R:49:40:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/ggplot2-themes.R#L49) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        line = element_line(size = .75*(.75/1.6), lineend = 'round'),
                                       ^
```
[R/ggplot2-themes.R:49:44:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/ggplot2-themes.R#L49) *style:* **Put spaces around all infix operators.**
```r
        line = element_line(size = .75*(.75/1.6), lineend = 'round'),
                                          ~^~
```
[R/ggplot2-themes.R:57:63:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/ggplot2-themes.R#L57) *style:* **Put spaces around all infix operators.**
```r
        axis.line.x = element_line(color = 'black', size = .75*(.75/1.6), lineend = 'round'),
                                                             ~^~
```
[R/ggplot2-themes.R:57:64:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/ggplot2-themes.R#L57) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        axis.line.x = element_line(color = 'black', size = .75*(.75/1.6), lineend = 'round'),
                                                               ^
```
[R/ggplot2-themes.R:57:68:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/ggplot2-themes.R#L57) *style:* **Put spaces around all infix operators.**
```r
        axis.line.x = element_line(color = 'black', size = .75*(.75/1.6), lineend = 'round'),
                                                                  ~^~
```
[R/ggplot2-themes.R:58:63:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/ggplot2-themes.R#L58) *style:* **Put spaces around all infix operators.**
```r
        axis.line.y = element_line(color = 'black', size = .75*(.75/1.6), lineend = 'round'),
                                                             ~^~
```
[R/ggplot2-themes.R:58:64:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/ggplot2-themes.R#L58) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        axis.line.y = element_line(color = 'black', size = .75*(.75/1.6), lineend = 'round'),
                                                               ^
```
[R/ggplot2-themes.R:58:68:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/ggplot2-themes.R#L58) *style:* **Put spaces around all infix operators.**
```r
        axis.line.y = element_line(color = 'black', size = .75*(.75/1.6), lineend = 'round'),
                                                                  ~^~
```
[R/ggplot2-themes.R:60:64:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/ggplot2-themes.R#L60) *style:* **Put spaces around all infix operators.**
```r
        axis.ticks.x = element_line(color = 'black', size = .75*(.75/1.6), lineend = 'round'),
                                                              ~^~
```
[R/ggplot2-themes.R:60:65:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/ggplot2-themes.R#L60) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        axis.ticks.x = element_line(color = 'black', size = .75*(.75/1.6), lineend = 'round'),
                                                                ^
```
[R/ggplot2-themes.R:60:69:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/ggplot2-themes.R#L60) *style:* **Put spaces around all infix operators.**
```r
        axis.ticks.x = element_line(color = 'black', size = .75*(.75/1.6), lineend = 'round'),
                                                                   ~^~
```
[R/ggplot2-themes.R:61:64:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/ggplot2-themes.R#L61) *style:* **Put spaces around all infix operators.**
```r
        axis.ticks.y = element_line(color = 'black', size = .75*(.75/1.6), lineend = 'round'),
                                                              ~^~
```
[R/ggplot2-themes.R:61:65:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/ggplot2-themes.R#L61) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        axis.ticks.y = element_line(color = 'black', size = .75*(.75/1.6), lineend = 'round'),
                                                                ^
```
[R/ggplot2-themes.R:61:69:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/ggplot2-themes.R#L61) *style:* **Put spaces around all infix operators.**
```r
        axis.ticks.y = element_line(color = 'black', size = .75*(.75/1.6), lineend = 'round'),
                                                                   ~^~
```
[R/ggplot2-themes.R:67:35:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/ggplot2-themes.R#L67) *style:* **Commas should always have a space after.**
```r
        plot.margin = unit(c(0.25,0.5,0.25,0.25), 'lines')
                                  ^
```
[R/ggplot2-themes.R:67:39:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/ggplot2-themes.R#L67) *style:* **Commas should always have a space after.**
```r
        plot.margin = unit(c(0.25,0.5,0.25,0.25), 'lines')
                                      ^
```
[R/ggplot2-themes.R:67:44:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/ggplot2-themes.R#L67) *style:* **Commas should always have a space after.**
```r
        plot.margin = unit(c(0.25,0.5,0.25,0.25), 'lines')
                                           ^
```
[R/impact-genes.R:15:3:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/impact-genes.R#L15) *style:* **Commented code should be removed.**
```r
# impact_genes = fread('impact-468.txt')
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/impact-genes.R:16:3:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/impact-genes.R#L16) *style:* **Commented code should be removed.**
```r
# devtools::use_data(impact_genes)
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/kpjmisc.R:10:3:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/kpjmisc.R#L10) *style:* **Place a space before left parenthesis, except in a function call.**
```r
if(getRversion() >= "2.15.1")  utils::globalVariables(c("."), add = FALSE)
  ^
```
[R/mutation-types.R:11:3:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/mutation-types.R#L11) *style:* **Commented code should be removed.**
```r
# save(coding_mutations, file = 'data/coding_mutations.rda')
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mutation-types.R:18:3:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/mutation-types.R#L18) *style:* **Commented code should be removed.**
```r
# save(truncating_mutations, file = 'data/truncating_mutations.rda')
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot-stratton.R:15:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L15) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
{
^
```
[R/plot-stratton.R:49:41:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L49) *style:* **Commas should always have a space after.**
```r
            Reference_Allele %in% c('C','T'),
                                        ^
```
[R/plot-stratton.R:50:36:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L50) *style:* **Commas should always have a space after.**
```r
            paste0(str_sub(Ref_Tri,1,2),Tumor_Seq_Allele2,str_sub(Ref_Tri,3,3)),
                                   ^
```
[R/plot-stratton.R:50:38:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L50) *style:* **Commas should always have a space after.**
```r
            paste0(str_sub(Ref_Tri,1,2),Tumor_Seq_Allele2,str_sub(Ref_Tri,3,3)),
                                     ^
```
[R/plot-stratton.R:50:41:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L50) *style:* **Commas should always have a space after.**
```r
            paste0(str_sub(Ref_Tri,1,2),Tumor_Seq_Allele2,str_sub(Ref_Tri,3,3)),
                                        ^
```
[R/plot-stratton.R:50:59:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L50) *style:* **Commas should always have a space after.**
```r
            paste0(str_sub(Ref_Tri,1,2),Tumor_Seq_Allele2,str_sub(Ref_Tri,3,3)),
                                                          ^
```
[R/plot-stratton.R:50:75:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L50) *style:* **Commas should always have a space after.**
```r
            paste0(str_sub(Ref_Tri,1,2),Tumor_Seq_Allele2,str_sub(Ref_Tri,3,3)),
                                                                          ^
```
[R/plot-stratton.R:50:77:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L50) *style:* **Commas should always have a space after.**
```r
            paste0(str_sub(Ref_Tri,1,2),Tumor_Seq_Allele2,str_sub(Ref_Tri,3,3)),
                                                                            ^
```
[R/plot-stratton.R:51:36:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L51) *style:* **Commas should always have a space after.**
```r
            paste0(str_sub(Ref_Tri,1,1),nt_comp[Reference_Allele],nt_comp[Tumor_Seq_Allele2],str_sub(Ref_Tri,3,3)))) %>%
                                   ^
```
[R/plot-stratton.R:51:38:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L51) *style:* **Commas should always have a space after.**
```r
            paste0(str_sub(Ref_Tri,1,1),nt_comp[Reference_Allele],nt_comp[Tumor_Seq_Allele2],str_sub(Ref_Tri,3,3)))) %>%
                                     ^
```
[R/plot-stratton.R:51:41:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L51) *style:* **Commas should always have a space after.**
```r
            paste0(str_sub(Ref_Tri,1,1),nt_comp[Reference_Allele],nt_comp[Tumor_Seq_Allele2],str_sub(Ref_Tri,3,3)))) %>%
                                        ^
```
[R/plot-stratton.R:51:67:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L51) *style:* **Commas should always have a space after.**
```r
            paste0(str_sub(Ref_Tri,1,1),nt_comp[Reference_Allele],nt_comp[Tumor_Seq_Allele2],str_sub(Ref_Tri,3,3)))) %>%
                                                                  ^
```
[R/plot-stratton.R:51:94:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L51) *style:* **Commas should always have a space after.**
```r
            paste0(str_sub(Ref_Tri,1,1),nt_comp[Reference_Allele],nt_comp[Tumor_Seq_Allele2],str_sub(Ref_Tri,3,3)))) %>%
                                                                                ^
```
[R/plot-stratton.R:51:110:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L51) *style:* **Commas should always have a space after.**
```r
            paste0(str_sub(Ref_Tri,1,1),nt_comp[Reference_Allele],nt_comp[Tumor_Seq_Allele2],str_sub(Ref_Tri,3,3)))) %>%
                                                                                ^
```
[R/plot-stratton.R:51:112:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L51) *style:* **Commas should always have a space after.**
```r
            paste0(str_sub(Ref_Tri,1,1),nt_comp[Reference_Allele],nt_comp[Tumor_Seq_Allele2],str_sub(Ref_Tri,3,3)))) %>%
                                                                                ^
```
[R/plot-stratton.R:52:39:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L52) *style:* **Commas should always have a space after.**
```r
        filter(str_sub(TriNuc_Context,2,2) != str_sub(TriNuc_Context,3,3)) %>%
                                      ^
```
[R/plot-stratton.R:52:41:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L52) *style:* **Commas should always have a space after.**
```r
        filter(str_sub(TriNuc_Context,2,2) != str_sub(TriNuc_Context,3,3)) %>%
                                        ^
```
[R/plot-stratton.R:52:70:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L52) *style:* **Commas should always have a space after.**
```r
        filter(str_sub(TriNuc_Context,2,2) != str_sub(TriNuc_Context,3,3)) %>%
                                                                     ^
```
[R/plot-stratton.R:52:72:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L52) *style:* **Commas should always have a space after.**
```r
        filter(str_sub(TriNuc_Context,2,2) != str_sub(TriNuc_Context,3,3)) %>%
                                                                       ^
```
[R/plot-stratton.R:57:42:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L57) *style:* **Put spaces around all infix operators.**
```r
        mutate(TriNuc_Frac = TriNuc_Count/sum(TriNuc_Count)) %>%
                                        ~^~
```
[R/plot-stratton.R:59:59:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L59) *style:* **Commas should always have a space after.**
```r
        mutate(Transition = paste0(str_sub(TriNuc_Context,2,2),'>',str_sub(TriNuc_Context,3,3)))
                                                          ^
```
[R/plot-stratton.R:59:61:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L59) *style:* **Commas should always have a space after.**
```r
        mutate(Transition = paste0(str_sub(TriNuc_Context,2,2),'>',str_sub(TriNuc_Context,3,3)))
                                                            ^
```
[R/plot-stratton.R:59:64:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L59) *style:* **Commas should always have a space after.**
```r
        mutate(Transition = paste0(str_sub(TriNuc_Context,2,2),'>',str_sub(TriNuc_Context,3,3)))
                                                               ^
```
[R/plot-stratton.R:59:68:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L59) *style:* **Commas should always have a space after.**
```r
        mutate(Transition = paste0(str_sub(TriNuc_Context,2,2),'>',str_sub(TriNuc_Context,3,3)))
                                                                   ^
```
[R/plot-stratton.R:59:91:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L59) *style:* **Commas should always have a space after.**
```r
        mutate(Transition = paste0(str_sub(TriNuc_Context,2,2),'>',str_sub(TriNuc_Context,3,3)))
                                                                                ^
```
[R/plot-stratton.R:59:93:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L59) *style:* **Commas should always have a space after.**
```r
        mutate(Transition = paste0(str_sub(TriNuc_Context,2,2),'>',str_sub(TriNuc_Context,3,3)))
                                                                                ^
```
[R/plot-stratton.R:71:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L71) *style:* **Lines should not be more than 120 characters.**
```r
        scale_x_discrete(labels = paste0(str_sub(levels(trinuc_maf$TriNuc_Context),1,2), str_sub(levels(trinuc_maf$TriNuc_Context),4,4))) +
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot-stratton.R:71:84:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L71) *style:* **Commas should always have a space after.**
```r
        scale_x_discrete(labels = paste0(str_sub(levels(trinuc_maf$TriNuc_Context),1,2), str_sub(levels(trinuc_maf$TriNuc_Context),4,4))) +
                                                                                ^
```
[R/plot-stratton.R:71:86:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L71) *style:* **Commas should always have a space after.**
```r
        scale_x_discrete(labels = paste0(str_sub(levels(trinuc_maf$TriNuc_Context),1,2), str_sub(levels(trinuc_maf$TriNuc_Context),4,4))) +
                                                                                ^
```
[R/plot-stratton.R:71:132:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L71) *style:* **Commas should always have a space after.**
```r
        scale_x_discrete(labels = paste0(str_sub(levels(trinuc_maf$TriNuc_Context),1,2), str_sub(levels(trinuc_maf$TriNuc_Context),4,4))) +
                                                                                ^
```
[R/plot-stratton.R:71:134:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L71) *style:* **Commas should always have a space after.**
```r
        scale_x_discrete(labels = paste0(str_sub(levels(trinuc_maf$TriNuc_Context),1,2), str_sub(levels(trinuc_maf$TriNuc_Context),4,4))) +
                                                                                ^
```
[R/plot-stratton.R:74:41:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L74) *style:* **Commas should always have a space after.**
```r
        scale_y_continuous(expand = c(0,0)) # +
                                        ^
```
[R/plot-stratton.R:75:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L75) *style:* **Lines should not be more than 120 characters.**
```r
        #geom_hline(yintercept = seq(0, max(as.numeric(trinuc_maf$TriNuc_Frac)), .05), col = 'white', size = .5, alpha = .5)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot-stratton.R:75:10:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-stratton.R#L75) *style:* **Commented code should be removed.**
```r
        #geom_hline(yintercept = seq(0, max(as.numeric(trinuc_maf$TriNuc_Frac)), .05), col = 'white', size = .5, alpha = .5)
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot-survival.R:34:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L34) *style:* **Use spaces to indent, not tabs.**
```r
	# Tidy data frame
^
```
[R/plot-survival.R:35:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L35) *style:* **Use spaces to indent, not tabs.**
```r
	sf = tidy(survfit_object)
^
```
[R/plot-survival.R:36:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L36) *style:* **Use spaces to indent, not tabs.**
```r
	if (!'strata' %in% names(sf)) sf$strata = ''
^
```
[R/plot-survival.R:38:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L38) *style:* **Use spaces to indent, not tabs.**
```r
	# Add start at 0, by stratum
^
```
[R/plot-survival.R:39:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L39) *style:* **Use spaces to indent, not tabs.**
```r
	top_rows = ldply(unique(sf$strata), function(s) {
^
```
[R/plot-survival.R:40:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L40) *style:* **Use spaces to indent, not tabs.**
```r
		sf_s = filter(sf, strata == s)
^~
```
[R/plot-survival.R:41:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L41) *style:* **Use spaces to indent, not tabs.**
```r
		c(strata = s, time = 0, n.risk = max(sf_s$n.risk),
^~
```
[R/plot-survival.R:42:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L42) *style:* **Use spaces to indent, not tabs.**
```r
			n.event = 0, n.censor = 0, estimate = 1, conf.high = 1, conf.low = 1)
^~~
```
[R/plot-survival.R:43:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L43) *style:* **Use spaces to indent, not tabs.**
```r
		})
^~
```
[R/plot-survival.R:45:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L45) *style:* **Use spaces to indent, not tabs.**
```r
	rbind.fill(sf, top_rows) %>%
^
```
[R/plot-survival.R:46:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L46) *style:* **Use spaces to indent, not tabs.**
```r
		mutate_at(vars(estimate, time), funs(as.numeric(.))) %>%
^~
```
[R/plot-survival.R:47:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L47) *style:* **Use spaces to indent, not tabs.**
```r
	    arrange(strata, time, desc(estimate))
^
```
[R/plot-survival.R:53:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L53) *style:* **Use spaces to indent, not tabs.**
```r
	survfit_object,
^
```
[R/plot-survival.R:54:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L54) *style:* **Use spaces to indent, not tabs.**
```r
	colors = NULL,
^
```
[R/plot-survival.R:55:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L55) *style:* **Use spaces to indent, not tabs.**
```r
	legend_title = NULL,
^
```
[R/plot-survival.R:56:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L56) *style:* **Use spaces to indent, not tabs.**
```r
	plot_title = NULL,
^
```
[R/plot-survival.R:57:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L57) *style:* **Use spaces to indent, not tabs.**
```r
	xmax = NULL,
^
```
[R/plot-survival.R:58:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L58) *style:* **Use spaces to indent, not tabs.**
```r
	parse_strata = FALSE,
^
```
[R/plot-survival.R:59:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L59) *style:* **Use spaces to indent, not tabs.**
```r
	x_lab = NULL,
^
```
[R/plot-survival.R:60:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L60) *style:* **Use spaces to indent, not tabs.**
```r
	y_lab = NULL,
^
```
[R/plot-survival.R:61:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L61) *style:* **Use spaces to indent, not tabs.**
```r
	legend_pos = NULL,
^
```
[R/plot-survival.R:62:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L62) *style:* **Use spaces to indent, not tabs.**
```r
	pval = TRUE,
^
```
[R/plot-survival.R:63:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L63) *style:* **Use spaces to indent, not tabs.**
```r
	pval_pos = NULL,
^
```
[R/plot-survival.R:64:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L64) *style:* **Use spaces to indent, not tabs.**
```r
	interval = NULL,
^
```
[R/plot-survival.R:65:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L65) *style:* **Use spaces to indent, not tabs.**
```r
	env_theme = TRUE,
^
```
[R/plot-survival.R:66:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L66) *style:* **Use spaces to indent, not tabs.**
```r
	table = FALSE
^
```
[R/plot-survival.R:67:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L67) *style:* **Use spaces to indent, not tabs.**
```r
	) {
^
```
[R/plot-survival.R:71:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L71) *style:* **Use spaces to indent, not tabs.**
```r
	if (is.null(legend_title)) {
^
```
[R/plot-survival.R:72:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L72) *style:* **Use spaces to indent, not tabs.**
```r
		# legend_title = stringi::stri_trans_totitle(str_extract(names(survfit_object$strata), '^.*(?=\\=)')[1])
^~
```
[R/plot-survival.R:72:5:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L72) *style:* **Commented code should be removed.**
```r
		# legend_title = stringi::stri_trans_totitle(str_extract(names(survfit_object$strata), '^.*(?=\\=)')[1])
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot-survival.R:73:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L73) *style:* **Use spaces to indent, not tabs.**
```r
		legend_title = ''
^~
```
[R/plot-survival.R:74:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L74) *style:* **Use spaces to indent, not tabs.**
```r
	}
^
```
[R/plot-survival.R:75:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L75) *style:* **Use spaces to indent, not tabs.**
```r
	if (length(survfit_object$strata)>1) {
^
```
[R/plot-survival.R:75:35:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L75) *style:* **Put spaces around all infix operators.**
```r
	if (length(survfit_object$strata)>1) {
                                 ~^~
```
[R/plot-survival.R:76:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L76) *style:* **Use spaces to indent, not tabs.**
```r
		# s_labels = str_c(str_extract(names(survfit_object$strata), '(?<==).*'), ' (n=', survfit_object$n, ')')
^~
```
[R/plot-survival.R:76:5:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L76) *style:* **Commented code should be removed.**
```r
		# s_labels = str_c(str_extract(names(survfit_object$strata), '(?<==).*'), ' (n=', survfit_object$n, ')')
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plot-survival.R:77:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L77) *style:* **Use spaces to indent, not tabs.**
```r
	    s_labels = str_c(str_extract(names(survfit_object$strata), '(?<==).*'))
^
```
[R/plot-survival.R:78:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L78) *style:* **Use spaces to indent, not tabs.**
```r
		if (parse_strata) s_labels = str_replace(s_labels, c('FALSE|0','TRUE|1'), c('WT','Mut'))
^~
```
[R/plot-survival.R:78:66:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L78) *style:* **Commas should always have a space after.**
```r
		if (parse_strata) s_labels = str_replace(s_labels, c('FALSE|0','TRUE|1'), c('WT','Mut'))
                                                                 ^
```
[R/plot-survival.R:78:84:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L78) *style:* **Commas should always have a space after.**
```r
		if (parse_strata) s_labels = str_replace(s_labels, c('FALSE|0','TRUE|1'), c('WT','Mut'))
                                                                                ^
```
[R/plot-survival.R:79:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L79) *style:* **Use spaces to indent, not tabs.**
```r
		sf = mutate(sf, strata = mapvalues(strata, names(survfit_object$strata), s_labels))
^~
```
[R/plot-survival.R:80:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L80) *style:* **Use spaces to indent, not tabs.**
```r
		names(survfit_object$strata) = str_extract(names(survfit_object$strata), '(?<==).*')
^~
```
[R/plot-survival.R:81:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L81) *style:* **Use spaces to indent, not tabs.**
```r
	} else {
^
```
[R/plot-survival.R:82:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L82) *style:* **Use spaces to indent, not tabs.**
```r
		sf$strata = ''
^~
```
[R/plot-survival.R:83:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L83) *style:* **Use spaces to indent, not tabs.**
```r
		s_labels = str_c('n=', survfit_object$n)
^~
```
[R/plot-survival.R:84:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L84) *style:* **Use spaces to indent, not tabs.**
```r
		legend_pos = 'none'
^~
```
[R/plot-survival.R:85:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L85) *style:* **Use spaces to indent, not tabs.**
```r
	}
^
```
[R/plot-survival.R:87:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L87) *style:* **Use spaces to indent, not tabs.**
```r
	if (is.null(x_lab)) x_lab = 'Time'
^
```
[R/plot-survival.R:88:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L88) *style:* **Use spaces to indent, not tabs.**
```r
	if (is.null(y_lab)) y_lab = 'Survival function'
^
```
[R/plot-survival.R:89:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L89) *style:* **Use spaces to indent, not tabs.**
```r
	if (is.null(xmax)) {
^
```
[R/plot-survival.R:90:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L90) *style:* **Use spaces to indent, not tabs.**
```r
	    xmax = 1.04*max(sf$time)
^
```
[R/plot-survival.R:90:17:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L90) *style:* **Put spaces around all infix operators.**
```r
	    xmax = 1.04*max(sf$time)
               ~^~
```
[R/plot-survival.R:91:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L91) *style:* **Use spaces to indent, not tabs.**
```r
	} else {
^
```
[R/plot-survival.R:92:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L92) *style:* **Use spaces to indent, not tabs.**
```r
	    sf = filter(sf, time <= xmax) %>%
^
```
[R/plot-survival.R:93:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L93) *style:* **Use spaces to indent, not tabs.**
```r
	        add_row(strata = unique(sf$strata), time = xmax) %>%
^
```
[R/plot-survival.R:94:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L94) *style:* **Use spaces to indent, not tabs.**
```r
	        arrange(strata, time) %>%
^
```
[R/plot-survival.R:95:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L95) *style:* **Use spaces to indent, not tabs.**
```r
	        tidyr::fill(n.risk, n.event, n.censor, estimate) %>%
^
```
[R/plot-survival.R:96:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L96) *style:* **Use spaces to indent, not tabs.**
```r
	        group_by(strata) %>%
^
```
[R/plot-survival.R:97:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L97) *style:* **Use spaces to indent, not tabs.**
```r
	        filter(
^
```
[R/plot-survival.R:98:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L98) *style:* **Use spaces to indent, not tabs.**
```r
	            !( (time == xmax & n.risk == n.event) & (lag(n.risk) == lag(n.event) )) &
^
```
[R/plot-survival.R:98:16:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L98) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
	            !( (time == xmax & n.risk == n.event) & (lag(n.risk) == lag(n.event) )) &
               ^
```
[R/plot-survival.R:98:82:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L98) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
	            !( (time == xmax & n.risk == n.event) & (lag(n.risk) == lag(n.event) )) &
                                                                                ^
```
[R/plot-survival.R:99:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L99) *style:* **Use spaces to indent, not tabs.**
```r
	            !(time == xmax & lag(n.risk) == 1 & lag(n.censor) == 1)) %>%
^
```
[R/plot-survival.R:100:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L100) *style:* **Use spaces to indent, not tabs.**
```r
	        ungroup
^
```
[R/plot-survival.R:101:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L101) *style:* **Use spaces to indent, not tabs.**
```r
	}
^
```
[R/plot-survival.R:104:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L104) *style:* **Use spaces to indent, not tabs.**
```r
	sf_plot = ggplot(data = sf) +
^
```
[R/plot-survival.R:105:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L105) *style:* **Use spaces to indent, not tabs.**
```r
		geom_step(aes(x = time, y = estimate, group = strata, color = strata), direction = 'hv') +
^~
```
[R/plot-survival.R:106:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L106) *style:* **Use spaces to indent, not tabs.**
```r
		geom_point(data = filter(sf, n.censor == 1), aes(x = time, y = estimate, color = strata), shape= '|',
^~
```
[R/plot-survival.R:106:98:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L106) *style:* **Put spaces around all infix operators.**
```r
		geom_point(data = filter(sf, n.censor == 1), aes(x = time, y = estimate, color = strata), shape= '|',
                                                                                ~^
```
[R/plot-survival.R:107:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L107) *style:* **Use spaces to indent, not tabs.**
```r
			show.legend = F) +
^~~
```
[R/plot-survival.R:108:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L108) *style:* **Use spaces to indent, not tabs.**
```r
	    scale_y_continuous(expand = c(0,0), limits = c(-.01,1.04),
^
```
[R/plot-survival.R:108:38:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L108) *style:* **Commas should always have a space after.**
```r
	    scale_y_continuous(expand = c(0,0), limits = c(-.01,1.04),
                                     ^
```
[R/plot-survival.R:108:58:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L108) *style:* **Commas should always have a space after.**
```r
	    scale_y_continuous(expand = c(0,0), limits = c(-.01,1.04),
                                                         ^
```
[R/plot-survival.R:109:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L109) *style:* **Use spaces to indent, not tabs.**
```r
	                       breaks = seq(0, 1, .25), labels = function(x) 100*x) +
^
```
[R/plot-survival.R:109:74:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L109) *style:* **Put spaces around all infix operators.**
```r
	                       breaks = seq(0, 1, .25), labels = function(x) 100*x) +
                                                                        ~^~
```
[R/plot-survival.R:110:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L110) *style:* **Use spaces to indent, not tabs.**
```r
	    scale_color_manual(values = brewer.pal(8, 'Paired'),
^
```
[R/plot-survival.R:111:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L111) *style:* **Use spaces to indent, not tabs.**
```r
	                       labels = function(x) {
^
```
[R/plot-survival.R:112:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L112) *style:* **Use spaces to indent, not tabs.**
```r
	                           str_c(x, ' (n=', survfit_object$n[match(x, names(survfit_object$strata))], ')')
^
```
[R/plot-survival.R:113:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L113) *style:* **Use spaces to indent, not tabs.**
```r
	                       }) +
^
```
[R/plot-survival.R:114:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L114) *style:* **Use spaces to indent, not tabs.**
```r
		theme(line = element_line(lineend = 'round'),
^~
```
[R/plot-survival.R:115:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L115) *style:* **Use spaces to indent, not tabs.**
```r
		      legend.position = c(1,1), legend.justification = c(1,1),
^~
```
[R/plot-survival.R:115:31:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L115) *style:* **Commas should always have a space after.**
```r
		      legend.position = c(1,1), legend.justification = c(1,1),
                              ^
```
[R/plot-survival.R:115:62:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L115) *style:* **Commas should always have a space after.**
```r
		      legend.position = c(1,1), legend.justification = c(1,1),
                                                             ^
```
[R/plot-survival.R:116:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L116) *style:* **Use spaces to indent, not tabs.**
```r
		      legend.title = element_text(size = theme_get()$legend.text$size),
^~
```
[R/plot-survival.R:117:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L117) *style:* **Use spaces to indent, not tabs.**
```r
		      legend.text = element_text(size = theme_get()$legend.text$size),
^~
```
[R/plot-survival.R:118:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L118) *style:* **Use spaces to indent, not tabs.**
```r
		      axis.line.x = element_blank(),
^~
```
[R/plot-survival.R:119:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L119) *style:* **Use spaces to indent, not tabs.**
```r
		      axis.line.y = element_blank(),
^~
```
[R/plot-survival.R:120:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L120) *style:* **Use spaces to indent, not tabs.**
```r
		      # panel.border = element_rect(size = .75, color = 'black', linetype = 'solid', fill = NA),
^~
```
[R/plot-survival.R:121:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L121) *style:* **Use spaces to indent, not tabs.**
```r
		      panel.background = element_rect(fill = NA),
^~
```
[R/plot-survival.R:122:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L122) *style:* **Use spaces to indent, not tabs.**
```r
		      plot.title = element_text(vjust = -1),
^~
```
[R/plot-survival.R:123:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L123) *style:* **Use spaces to indent, not tabs.**
```r
		      aspect.ratio = 1) +
^~
```
[R/plot-survival.R:124:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L124) *style:* **Use spaces to indent, not tabs.**
```r
		labs(x = x_lab, y = y_lab, color = legend_title) +
^~
```
[R/plot-survival.R:125:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L125) *style:* **Use spaces to indent, not tabs.**
```r
	    coord_cartesian(clip = 'off')
^
```
[R/plot-survival.R:127:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L127) *style:* **Use spaces to indent, not tabs.**
```r
	if (!is.null(interval)) {
^
```
[R/plot-survival.R:128:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L128) *style:* **Use spaces to indent, not tabs.**
```r
	    sf_plot = sf_plot +
^
```
[R/plot-survival.R:129:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L129) *style:* **Use spaces to indent, not tabs.**
```r
	        scale_x_continuous(expand = c(.01,0), limits = c(0, xmax), breaks = seq(0, xmax, interval))
^
```
[R/plot-survival.R:129:44:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L129) *style:* **Commas should always have a space after.**
```r
	        scale_x_continuous(expand = c(.01,0), limits = c(0, xmax), breaks = seq(0, xmax, interval))
                                           ^
```
[R/plot-survival.R:130:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L130) *style:* **Use spaces to indent, not tabs.**
```r
	} else {
^
```
[R/plot-survival.R:132:47:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L132) *style:* **Commas should always have a space after.**
```r
            scale_x_continuous(expand = c(.01,0), limits = c(0, xmax), breaks = scales::pretty_breaks(n = 4))
                                              ^
```
[R/plot-survival.R:133:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L133) *style:* **Use spaces to indent, not tabs.**
```r
	}
^
```
[R/plot-survival.R:135:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L135) *style:* **Use spaces to indent, not tabs.**
```r
	# Calculate p-value
^
```
[R/plot-survival.R:136:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L136) *style:* **Use spaces to indent, not tabs.**
```r
	if (pval & length(survfit_object$strata)>1) {
^
```
[R/plot-survival.R:136:42:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L136) *style:* **Put spaces around all infix operators.**
```r
	if (pval & length(survfit_object$strata)>1) {
                                        ~^~
```
[R/plot-survival.R:137:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L137) *style:* **Use spaces to indent, not tabs.**
```r
	    sf_call = as.character(survfit_object$call)
^
```
[R/plot-survival.R:138:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L138) *style:* **Use spaces to indent, not tabs.**
```r
	    sf_call = paste0(gsub('survfit', 'survdiff', sf_call[1]), '(', sf_call[2], ',data=', sf_call[3],')')
^
```
[R/plot-survival.R:138:102:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L138) *style:* **Commas should always have a space after.**
```r
	    sf_call = paste0(gsub('survfit', 'survdiff', sf_call[1]), '(', sf_call[2], ',data=', sf_call[3],')')
                                                                                ^
```
[R/plot-survival.R:139:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L139) *style:* **Use spaces to indent, not tabs.**
```r
	    sd = eval(parse(text = sf_call))
^
```
[R/plot-survival.R:140:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L140) *style:* **Use spaces to indent, not tabs.**
```r
	    pval = 1 - pchisq(sd$chisq, length(sd$n) - 1)
^
```
[R/plot-survival.R:141:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L141) *style:* **Use spaces to indent, not tabs.**
```r
	    if (pval <= 1e-03) { pval = scales::scientific_format(digits = 3)(pval) } else { pval = round(pval, 3) }
^
```
[R/plot-survival.R:141:25:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L141) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
	    if (pval <= 1e-03) { pval = scales::scientific_format(digits = 3)(pval) } else { pval = round(pval, 3) }
                        ^
```
[R/plot-survival.R:141:78:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L141) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
	    if (pval <= 1e-03) { pval = scales::scientific_format(digits = 3)(pval) } else { pval = round(pval, 3) }
                                                                             ^
```
[R/plot-survival.R:141:85:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L141) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
	    if (pval <= 1e-03) { pval = scales::scientific_format(digits = 3)(pval) } else { pval = round(pval, 3) }
                                                                                ^
```
[R/plot-survival.R:141:109:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L141) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
	    if (pval <= 1e-03) { pval = scales::scientific_format(digits = 3)(pval) } else { pval = round(pval, 3) }
                                                                                ^
```
[R/plot-survival.R:142:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L142) *style:* **Use spaces to indent, not tabs.**
```r
	    if (length(unique(sf$strata))==2) {
^
```
[R/plot-survival.R:142:35:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L142) *style:* **Put spaces around all infix operators.**
```r
	    if (length(unique(sf$strata))==2) {
                                 ~^~~
```
[R/plot-survival.R:143:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L143) *style:* **Use spaces to indent, not tabs.**
```r
	        cp_call = gsub('survdiff', 'coxph', sf_call)
^
```
[R/plot-survival.R:144:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L144) *style:* **Use spaces to indent, not tabs.**
```r
	        cp = eval(parse(text = cp_call))
^
```
[R/plot-survival.R:145:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L145) *style:* **Use spaces to indent, not tabs.**
```r
	        hr = round(exp(cp$coefficients), 2)
^
```
[R/plot-survival.R:146:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L146) *style:* **Use spaces to indent, not tabs.**
```r
	        big_n = cp$n
^
```
[R/plot-survival.R:147:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L147) *style:* **Use spaces to indent, not tabs.**
```r
	        pval = str_c('N=', big_n, '\nHR=', hr, '\nP-value ', pval)
^
```
[R/plot-survival.R:148:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L148) *style:* **Use spaces to indent, not tabs.**
```r
	    } else {
^
```
[R/plot-survival.R:149:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L149) *style:* **Use spaces to indent, not tabs.**
```r
	    	big_n = sum(survfit_object$n)
^~~~~~
```
[R/plot-survival.R:150:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L150) *style:* **Use spaces to indent, not tabs.**
```r
	    	pval = str_c('N=', big_n, '\nP-value ', pval)
^~~~~~
```
[R/plot-survival.R:151:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L151) *style:* **Use spaces to indent, not tabs.**
```r
	    }
^
```
[R/plot-survival.R:152:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L152) *style:* **Use spaces to indent, not tabs.**
```r
	    if (is.null(pval_pos)) { pval_x = 0; pval_y = 0 } else { pval_x = pval_pos[1]; pval_y = pval_pos[2] }
^
```
[R/plot-survival.R:152:29:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L152) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
	    if (is.null(pval_pos)) { pval_x = 0; pval_y = 0 } else { pval_x = pval_pos[1]; pval_y = pval_pos[2] }
                            ^
```
[R/plot-survival.R:152:54:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L152) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
	    if (is.null(pval_pos)) { pval_x = 0; pval_y = 0 } else { pval_x = pval_pos[1]; pval_y = pval_pos[2] }
                                                     ^
```
[R/plot-survival.R:152:61:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L152) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
	    if (is.null(pval_pos)) { pval_x = 0; pval_y = 0 } else { pval_x = pval_pos[1]; pval_y = pval_pos[2] }
                                                            ^
```
[R/plot-survival.R:152:106:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L152) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
	    if (is.null(pval_pos)) { pval_x = 0; pval_y = 0 } else { pval_x = pval_pos[1]; pval_y = pval_pos[2] }
                                                                                ^
```
[R/plot-survival.R:153:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L153) *style:* **Use spaces to indent, not tabs.**
```r
	    sf_plot = sf_plot + annotate('text', x = pval_x, y = pval_y, label = pval,
^
```
[R/plot-survival.R:154:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L154) *style:* **Use spaces to indent, not tabs.**
```r
	                                 size = rel(2.5), vjust = -.25, hjust = 0, family = 'ArialMT')
^
```
[R/plot-survival.R:155:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L155) *style:* **Use spaces to indent, not tabs.**
```r
	    if (all(legend_pos==0)) legend_pos = c(1,1); legend_just = c(1,1)
^
```
[R/plot-survival.R:155:24:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L155) *style:* **Put spaces around all infix operators.**
```r
	    if (all(legend_pos==0)) legend_pos = c(1,1); legend_just = c(1,1)
                      ~^~~
```
[R/plot-survival.R:155:47:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L155) *style:* **Commas should always have a space after.**
```r
	    if (all(legend_pos==0)) legend_pos = c(1,1); legend_just = c(1,1)
                                              ^
```
[R/plot-survival.R:155:69:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L155) *style:* **Commas should always have a space after.**
```r
	    if (all(legend_pos==0)) legend_pos = c(1,1); legend_just = c(1,1)
                                                                    ^
```
[R/plot-survival.R:156:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L156) *style:* **Use spaces to indent, not tabs.**
```r
	}
^
```
[R/plot-survival.R:158:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L158) *style:* **Use spaces to indent, not tabs.**
```r
	sf_plot = sf_plot +
^
```
[R/plot-survival.R:159:1:](https://github.com/kpjonsson/kpjmisc/blob/6d7f043242e06c11e5acb73be1a0b3f454d868ad/R/plot-survival.R#L159) *style:* **Use spaces to indent, not tabs.**
```r
	    theme(legend.position = legend_pos, legend.justification = legend_just,
^
```


On line 30, a+KEY is very basic. It will shift ASCII characters across, but not rotate about the alphabet. E.g. A shift of +1 will move "Z" to "[".


Successfully aliased the URL <https://nteract-site-iscxrncmvd.now.sh> to the following alias.

* https://nteract.io


why did you revert this? Currently -4 is working well as far as I can see


> Considering to not make a release for that as it won't affect the code or test results.

indeed, make sense


images for SFBlegacy-size65.png & MS-Teams-Admin.png cannot be upload
error: File uploads require push access to this repository.


@OiTAvO sure!!!
Take a look[here](https://gist.github.com/joshbuchea/6f47e86d2510bce28f8e7f42ae84c716).


Successfully aliased the URL <https://fakeql-l6dkmy45k.now.sh> to the following aliases.

* https://fakeql.com
* https://www.fakeql.com
* https://fakeql-git-master.fredibach.now.sh


что то у вас с коментариями пошло не так


Successfully aliased the URL <https://react-frontend-developer-nhjeo60x0.now.sh> to the following aliases.

* https://react-frontend-developer.now.sh
* https://react-frontend-developer-git-master.charterhouse1.now.sh


было бы лучше если вы использовали отдельную функцию получения длины строки. Ну а в принципе можно проверить, что строка не пустая и взять sizeof


rename to `getColumnType` for clarity


> I don't think it is desired to support bare matrices without labels, The reason it was supported is probably only historical. Is this still used in documentation or actual FT code, or are you using this as undocumented feature yourself?
This is not used in documentation or FT code, but implemented in my pipeline by @schoffelen. I've already adapted my code to the neighbourhood description as in cfg2, but I thought I'd report this issue since it breaks the backward compatibility.


ну все классно. Но вместо сложной магии с индексами, на первый взгляд трудно читать, можно просто получить указатель на начало и на конец строки, и проверять до момента пока они не пересеклись, т.е. один инкрементируем, а другой декриментируем


`list(self.masters)  # Make sure that the UFOs are built` will take care of it, no?


ну переменные не пишут в основном с большой буквы


пишите операторы на отдельный строках


Deployment failed with the following error:

~~~
You defined 1 build that did not match any source files (please ensure they are NOT defined in .nowignore):
~~~


Начинаете писать комитам названия, а не оставлять дефолтные


Successfully aliased the URL <https://react-frontend-developer-8dtlm5afy.now.sh> to the following aliases.

* https://react-frontend-developer.now.sh
* https://react-frontend-developer-git-master.charterhouse1.now.sh


No use of `up_or_down` ? Maybe you want
```
calibrator_factor_func = lambda x: getattr(x,"corr_{}_JEC{}".format(group,up_or_down)) * x.rawFactor()
```


You are right Joytin, I forgot to update `Pipfile.lock` and that should be part of it. Thank you.


I like it.


если у вас в интерфейсе функции указано возращаемое значение, то его надо возращать


I need to develop a security application for a closed neighborhood which consists of 2 basic buttons that can send SMS. Very simple application and it will allow me to know the development process and the tools


Would that work for a binary from another pkg? I may give it a try…


matrices that reflect the spatial neighbourhood are in the cfg.connectivity field, to accommodate spatial relationships that are defined on a mesh of vertices, where the individual vertices do not necessarily have a label.


Nice! Wouldn't it make sense to flip it now though?

![](https://i.imgur.com/7vqJQz3.png)

The `bar` in `Test.hx` should be `foo`, not the other way around.


I had some very weird bugs, in which a repititive call to Write-Log would lead to CommandNotFoundException.
After switching out pretty much everything i identified the call to the targets as issue.
With Invoke-Command all bugs disappeared even under heavy load.


у вас если ввести строку больше размера то ваш код упадет


Is this change related to systematics?


have u done any change here


This commit brought more bugs than fixed.

1. If an infected quits and the number of infected is less than required minimum, humans do not get infected. Because of that it is possible that there will not be any zombies at all unless new people join or somebody dies. Do leavers get banned as we expect? I don't know.
2. Spectators auto-join the game after map change

This will be the third commit related to initial infection that we have to revert or heavily change. All three were heavy rewrites. All three were not reviewed. We should stop doing huge changes in order to fix bugs. Fixes should address one specific issue at a time, be small and reviewable. Nobody will review and test rewrites, including authors of the rewrites.


Thanks. Not working if you write to an img... however is working on plain canvas... I will work on a fix


Successfully aliased the URL <https://react-frontend-developer-hygivwr53.now.sh> to the following aliases.

* https://react-frontend-developer.now.sh
* https://react-frontend-developer-git-master.charterhouse1.now.sh


Please don't load the subscription on login. We don't need this data in the store and this just creates extra requests that will be blocking the loading of the page.


The build is green. Publishing ...


There is something that you do not want to understand with `delete_n_selected_rows`

It is there because of syntax of language may differ:

In English :
Delete 10 selected rows?

In German:
10 ausgewählte Zeilen löschen?


Successfully aliased the URL <https://100daysofsketches-yboldnhgcp.now.sh> to the following alias.

* https://100daysofsketches.com


Now could not deploy this pull request since the `now.json` file is empty.
It should be a valid JSON file.

    For more information on now.json visit https://zeit.co/docs/features/configuration#now.json.


Thanks for your reply. The problem was solved by your answer. But there appears some similar code problems. I find that it is due to the LLVM version. Some functions are not in LLVM 3.6.0 source code. I try to update LLVM version.
Does dg has the function of slicing instruction？ namely, instruction level. I want to know more about dg, but it is hard to find a detail introduction about dg.


Actually yes, genmatching is needed for tau energy scale. Genmatching was not done previously in embedding


Thanks for noticing this!


Thanks for your reply. The problem was solved by your answer. But there appears some similar code problems. I find that it is due to the LLVM version. Some functions are not in LLVM 3.6.0 source code. I try to update LLVM version.
Does dg has the function of slicing instruction？ namely, instruction level. I want to know more about dg, but it is hard to find a detail introduction about dg.  Where can I find more introduction about dg? Thank you.


Please note that os.Exit does not execute deferred watcher.Close()


Yes. And in this case %s was used. So translators change position %s in translated string. It's standard for translations.


That's great! You are a committed developer


I am not sure, but are the `#include`s at the top of this file really sufficient? It seems like we got a broken source.

See [the (probably) equivalent version of this file in Google's Android upstream kernel implementation of MediaTek](https://android.googlesource.com/kernel/mediatek/+/android-mtk-3.18/drivers/misc/mediatek/base/power/spm_v2/mt_spm_fs.c). Judging from the driver name & version (at the end of this file), it seems like this is the same driver.


Well seen, thanks!


The `.idea` folder is meant to be source controlled


## New strings
- `STREAM_ENDED: "This stream has ended"`
- `CLOSE_WINDOW: "Close Window"`
- `STREAM_NETWORK_QUALITY_ERROR: "Your network connection may be causing a decrease in video and audio quality. To improve voice audio, disable the stream."`
- `STREAM_RECONNECTING_ERROR: "You've been disconnected from the stream...sit tight, we're patching you back in!"`


Aqui creamos la mision de red sckull #7


2 empty lines here


Mse has many %s in code. You will understand it I hope.


del


April 5th


Successfully aliased the URL <https://paulkinlanme-cdznwoikj.now.sh> to the following aliases.

* https://paul.kinlan.me
* https://paulkinlanme-git-main.kinlan.now.sh


out your text in the the box then put the code in your bookmark url.


PushToV92 (energy-plus) - x86_64-Linux-Ubuntu-18.04-gcc-7.3: Tests Failed (677 of 3201 tests passed, 0 test warnings)

Failures:

integration Test Summary
 * Passed: 1
 * Failed: 659

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-21.15%25-red.png)


fixed here: 50307bb7ee3e8a20dec1695299fca0bbd4fd04be


try: [Pagination](https://codepen.io/cornflourblue/pen/oZZzLr)


Looks like a lowlevel attack impact, as the attacker can not reach other respondents. The resultexport can contain code, but that impact is low as well.  But still a fix needed and a reminder to all of us.


MY guy, your using Spring which means it creates and manages your objects, you should never initialise objects yourself, please remove everywhere where your creating object with the keyword "new", refactor the test to be a springboot Test, which means you can Autowire your dependencies...
Example  :

@RunWith(SpringJUnit4ClassRunner.class)
@SpringBootTest(classes = Application.class)
@Category(SpringIntegrationTests.class)
@WebAppConfiguration
@ActiveProfiles(profiles = "test")
public class RegistrationRequestTest {

    private final static Logger log = LoggerFactory.getLogger(RegistrationRequestTest.class);

	@Autowired
	private V1Worker v1Worker;
	@Autowired
	private RegistrationClient registrationClient;
}


Не забывать удалять данные перед миграцией, меняющей структуру таблиц.


Puzzle `510-d7a1e1df` discovered in   [`stroyprombeton/models.py`](  https://github.com/fidals/stroyprombeton/blob/master/stroyprombeton/models.py)   and submitted as #558. Please, remember that the puzzle was not   necessarily added in this particular commit. Maybe it was added earlier, but   we discovered it only now.


Puzzle `510-b8de40bc` discovered in   [`stroyprombeton/models.py`](  https://github.com/fidals/stroyprombeton/blob/master/stroyprombeton/models.py)   and submitted as #559. Please, remember that the puzzle was not   necessarily added in this particular commit. Maybe it was added earlier, but   we discovered it only now.


Puzzle `510-76a28a7b` discovered in   [`stroyprombeton/models.py`](  https://github.com/fidals/stroyprombeton/blob/master/stroyprombeton/models.py)   and submitted as #560. Please, remember that the puzzle was not   necessarily added in this particular commit. Maybe it was added earlier, but   we discovered it only now.


Update & Delete to go. ;)


ADDS THE ABILITY TO HAVE SEQUENCES AS KEYS, for keeping track of page numbers, versions, etc.etc.
Allows searches over these: for example find all pages > 5

ALSO: Adds the ability to automatically link or loop notes with hyperlinks

ALSO: Enhances the "project" functions... Functions automatically create sequence keys, and keep track of indexes...


Is this change related to systematic? Should mt and et channels be modified too?


@niksedk I know this is not the place to ask but I didn't want to open an issue for a question.
Is there a way to add a regex to user dictionary?
A while ago you made spell check warn when there is a number right after a word, like "Hey50".
But in Arabic, we write "The 5th" like this "الـ5", so we have "ـ" before the number and this is a known format even per Netflix's rules, so it there a way to add like "ـ\d+" to user dictionary?


Body can't be blank


I searched for `cfg.connectivity` but it turns out it is an undocumented option. The specification of it is all based on heuristics in ft_statistics_montecarlo. I propose that the `channelconnectivity(cfg)` call there is replaced by a proper ft_prepare_neighbours and a (new) neighbours2connectivity. That makes it more consistent.
But I still wonder whether cfg.connectivity is meant to be specified by the user, or whether it is just added to the cfg for easy passing around over different stats functions.


PushToV92 (energy-plus) - x86_64-Linux-Ubuntu-18.04-cppcheck-1.82: OK (0 of 0 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png)


simple primesquare() code that i've learned!


Changes are okay.


PushToV92 (energy-plus) - x86_64-Linux-Ubuntu-18.04-gcc-7.3-IntegrationCoverage-Debug: Tests Failed (2 of 2509 tests passed, 0 test warnings)

Failures:

integration Test Summary
 * Passed: 1
 * Failed: 659

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-0.08%25-red.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-0%25-red.png)


please remove the zipCode field (my bad, copy paste issue, it shouldn't be declared)


Reference to these drivers are completely removed from mtk's reference kernel from the latest ALPS. I've found only implementations for older chips.
Although I've found some messages about sodi3 in dmesg (only warnings),  seems it doesn't affect anything.


data path: `/vision/data/harbour`


How did you plan to convert
'Delete'
into
'',                 // ex_deletefiles
for German?
And what is 'Delete' for translator? Noun? Verb?
Is 'ausgewählte Zeilen löschen?' translation for 'selected rows?'. No, of cause.
Only %s is correct sollution.


PushToV92 (energy-plus) - x86_64-Linux-Ubuntu-18.04-custom_check: OK (3 of 3 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png)


Yup. Usually only one version per game, except for prototypes.


Now could not deploy this pull request since the `now.json` file does not contain valid JSON.

	Click here to see the contents of `now.json`

{"version":1.6.0,"name":"Graph_App","builds":[{"src":"package.json","use":"@now/static-build","config":{"distDir":"build"}}],"routes":[{"src":"/static/(.*)","headers":{"cache-control":"s-maxage=31536000,immutable"},"dest":"/static/$1"},{"src":"/favicon.ico","dest":"/favicon.ico"},{"src":"/asset-manifest.json","dest":"/asset-manifest.json"},{"src":"/manifest.json","dest":"/manifest.json"},{"src":"/precache-manifest.(.*)","dest":"/precache-manifest.$1"},{"src":"/service-worker.js","headers":{"cache-control":"s-maxage=0"},"dest":"/service-worker.js"},{"src":"/(.*)","headers":{"cache-control":"s-maxage=0"},"dest":"/index.html"}]}

For more information on now.json visit https://zeit.co/docs/features/configuration#now.json.


%>% は magrittr の関数ですので、magrittrを入れてみて下さい。
#43が解決すると、こういった問題はなくなります。