added function and test for aa_prop_bp.R

scripts/functions/aa_prop_bp.R

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+library(ggplot2)
+library(tidyverse)
+library(data.table)
+########################################################################
+# TASK: barplots to colour nssnps by chosen aa_property
+########################################################################
+aa_prop_bp <- function(plotdf
+                       , position_colname
+                       , fill_colname
+                       , fill_colours
+                       , leg_name = "LEGEND"){
+  mp = ggplot(df, aes(x = as.factor(eval(parse(text = pos_colname)))
+                      #, y = ..count..
+                      , fill = eval(parse(text = fill_colname))
+  )) +
+    geom_bar(position = 'identity') +
+    scale_fill_manual(values = fill_colours
+                      , name = leg_name)
+  return(mp)
+}
+
+

scripts/functions/test_aa_prop_bp.R

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+library(ggplot2)
+library(tidyverse)
+library(data.table)
+
+setwd("~/git/LSHTM_analysis/scripts/plotting/functions")
+getwd()
+#############################################################
+#===========================================
+# load functions, data, dirs, hardocded vars
+# that will be used in testing the functions
+#===========================================
+source("../plotting_data.R")
+infile = "/home/tanu/git/Data/streptomycin/output/"
+pd_df = plotting_data(infile)
+my_df       = pd_df[[1]]
+my_df_u     = pd_df[[2]]
+my_df_u_lig = pd_df[[3]]
+dup_muts    = pd_df[[4]]
+
+source("../plotting_globals.R")
+drug = "streptomycin"
+gene = "gid"
+
+import_dirs(drug, gene)
+
+#=====================
+# functions to test 
+#=====================
+source("stability_count_bp.R")
+source("position_count_bp.R")
+#################################################################
+##############################################
+# read a sample file containing muts and prop 
+###############################################
+df<- read.csv(file.choose())
+
+setDT(df)[, pos_count := .N, by = .(position)]
+foo = data.frame(df$position, df$pos_count)
+
+#snpsBYpos_df <- df %>%
+#  group_by(position) %>%
+#  summarize(snpsBYpos = mean(pos_count))
+
+# subset df without duplicates for position
+df2 = df[!duplicated(df$position)]
+##################################################################
+# ---------------------------------------
+# barplot for nssnps, coloured by aa prop
+# ---------------------------------------
+pos_colname = "position"
+aa_prop_colname = "mut_prop_water"
+aa_prop_colours = c("black", "blue")
+my_legname = "aa_prop: water"
+
+# call function
+aa_prop_bp(plotdf = df
+           , position_colname = pos_colname
+           , fill_colname = aa_prop_colname
+           , fill_colours = aa_prop_cols
+           , leg_name = my_legname)
+           
+#===============================================================