minor updates to dir.R

scripts/plotting/basic_barplots_PS.R

@@ -156,34 +156,7 @@ foo = select(df, mutationinformation
 svg(plot_pos_count_duet)
 print(paste0("plot filename:", plot_pos_count_duet))
 
-my_ats = 25 # axis text size
-my_als = 22 # axis label size
-
-# to make x axis display all positions
-# not sure if to use with sort or directly
-my_x = sort(unique(snpsBYpos_df$snpsBYpos)) 
-
-g = ggplot(snpsBYpos_df, aes(x = snpsBYpos))
-OutPlot_pos_count = g + geom_bar(aes (alpha = 0.5)
-                         , show.legend = FALSE) +
-  scale_x_continuous(breaks = unique(snpsBYpos_df$snpsBYpos)) +
-  #scale_x_continuous(breaks = my_x) +
-  geom_label(stat = "count", aes(label = ..count..)
-             , color = "black"
-             , size = 10) +
-  theme(axis.text.x = element_text(size = my_ats
-                                   , angle = 0)
-        , axis.text.y = element_text(size = my_ats
-                                     , angle = 0
-                                     , hjust = 1)
-        , axis.title.x = element_text(size = my_als)
-        , axis.title.y = element_text(size = my_als)
-        , plot.title = element_blank()) +
-  
-  labs(x = "Number of nsSNPs"
-       , y = "Number of Sites")
-
-print(OutPlot_pos_count)
+source("dirs.R")
 dev.off()
 ########################################################################
 #               			end of PS barplots         			   

scripts/plotting/dirs.R

@@ -12,10 +12,10 @@ import_dirs <- function(drug, gene) {
   #=============
   # directories and variables
   #=============
-  datadir        <<- paste0("~/git/Data")
-  indir          <<- paste0(datadir, "/", drug, "/input")
-  outdir         <<- paste0("~/git/Data", "/", drug, "/output")
-  plotdir        <<- paste0("~/git/Data", "/", drug, "/output/plots")
+  datadir        <<- paste0("~/git/Data/")
+  indir          <<- paste0(datadir, drug, "/input")
+  outdir         <<- paste0("~/git/Data/", drug, "/output")
+  plotdir        <<- paste0("~/git/Data/", drug, "/output/plots")
   
   dr_muts_col    <<- paste0('dr_mutations_', drug)
   other_muts_col <<- paste0('other_mutations_', drug)

scripts/plotting/plotting_data.R

@@ -15,8 +15,6 @@ library(ggplot2)
 library(data.table)
 library(dplyr)
 require("getopt", quietly = TRUE) #cmd parse arguments
-source("dirs.R")
-
 #========================================================
 # command line args
 spec = matrix(c(
@@ -37,8 +35,13 @@ gene = "gid"
 if(is.null(drug)|is.null(gene)) {
   stop("Missing arguments: --drug and --gene must both be specified (case-sensitive)")
 }
-
 #========================================================
+# Load functions
+# import dir structure
+source("dirs.R")
+import_dirs(drug, gene)
+#=======================================================
+
 #======
 # input
 #======