simplify the logic

pdimens · Nov 7, 2024 · b1cfddd · b1cfddd
1 parent a5bdc8f
commit b1cfddd
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Showing 6 changed files with 6 additions and 6 deletions.
diff --git a/harpy/reports/align_stats.Rmd b/harpy/reports/align_stats.Rmd
@@ -586,7 +586,7 @@ contigs <- group_by(tb, contig) %>%
   summarize(size = max(position)) %>%
   arrange(desc(size))
   
-if ((length(plot_contigs) == 1) && (plot_contigs[1] == "default")){
+if (all(plot_contigs == "default")){
   # limit the data to only the 30 largest contigs
   if (nrow(contigs) > 30){
     .contigs <- contigs[1:30, ]

diff --git a/harpy/reports/hapcut.Rmd b/harpy/reports/hapcut.Rmd
@@ -189,7 +189,7 @@ dropdown_buttons <- function(CONTIGS, CUTOFF = 0){
 
 ```{r plotting_contigs_setup}
 plotting_contigs <- snakemake@params$contigs
-if ((length(plotting_contigs) == 1) && (plotting_contigs[1] == "default")){
+if (all(plotting_contigs == "default")){
   .contigs <- group_by(df, contig) %>%
     summarize(size = max(pos_end)) %>%
     arrange(desc(size))

diff --git a/harpy/reports/leviathan.Rmd b/harpy/reports/leviathan.Rmd
@@ -208,7 +208,7 @@ fa.sizes <- read.table(fai, header = F) %>% arrange(desc(2))
 colnames(fa.sizes) <- c("contig", "size")
 
 plot_contigs <- snakemake@params$contigs
-if ((length(plot_contigs) == 1) && (plot_contigs[1] == "default")){
+if (all(plot_contigs == "default")){
   # make sure that the contigs with SV are the ones being plotted, not the others
   fa.sizes <- fa.sizes[fa.sizes$contig %in% unique(sv$contig), 1:2]
   # limit the data to only the 30 of the largest present contigs

diff --git a/harpy/reports/leviathan_pop.Rmd b/harpy/reports/leviathan_pop.Rmd
@@ -221,7 +221,7 @@ zooming on the plot.
 fa.sizes <- read.table(faidx, header = F)[,1:2] %>% arrange(desc(2))
 colnames(fa.sizes) <- c("contig", "size")
 plot_contigs <- snakemake@params$contigs
-if ((length(plot_contigs) == 1) && (plot_contigs[1] == "default")){
+if (all(plot_contigs == "default")){
   # make sure that the contigs with SV are the ones being plotted, not the others
   fa.sizes <- fa.sizes[fa.sizes$contig %in% unique(sv$contig), ]
   # limit the data to only the 30 of the largest present contigs

diff --git a/harpy/reports/naibr.Rmd b/harpy/reports/naibr.Rmd
@@ -291,7 +291,7 @@ ggplot(aes(x, y, fill = colour))+
 fa.sizes <- read.table(fai, header = F) %>% arrange(desc(2))
 colnames(fa.sizes) <- c("contig", "size")
 plot_contigs <- snakemake@params$contigs
-if ((length(plot_contigs) == 1) && (plot_contigs[1] == "default")){
+if (all(plot_contigs == "default")){
   # make sure that the contigs with SV are the ones being plotted, not the others
   fa.sizes <- fa.sizes[fa.sizes$contig %in% unique(sv$Chr1), 1:2]
   # limit the data to only the 30 of the largest present contigs

diff --git a/harpy/reports/naibr_pop.Rmd b/harpy/reports/naibr_pop.Rmd
@@ -293,7 +293,7 @@ zooming on the plot.
 fa.sizes <- read.table(fai, header = F) %>% arrange(desc(2))
 colnames(fa.sizes) <- c("contig", "size")
 plot_contigs <- snakemake@params$contigs
-if ((length(plot_contigs) == 1) && (plot_contigs[1] == "default")){
+if (all(plot_contigs == "default")){
   # make sure that the contigs with SV are the ones being plotted, not the others
   fa.sizes <- fa.sizes[fa.sizes$contig %in% unique(sv$Chr1), 1:2]
   # limit the data to only the 30 of the largest present contigs