lineage barplot script

scripts/plotting/combining_two_df.R

@@ -415,6 +415,7 @@ all.equal(foo, bar)
 #*************************
 # clear variables
 rm(foo, bar, gene_metadata
+   , in_filename_params, infile_params, merging_cols
    , merged_df2v2, merged_df2v3)
 
 #============================= end of script

scripts/plotting/lineage_basic_barplot.R

@@ -0,0 +1,218 @@
+#!/usr/bin/env Rscript       
+getwd()
+setwd("~/git/LSHTM_analysis/scripts/plotting/")
+getwd()
+#########################################################
+# TASK: Basic lineage barplot showing numbers
+
+# Output:
+
+##########################################################
+# 				Installing and loading required packages 			 
+##########################################################
+source("Header_TT.R")
+require(data.table)
+source("combining_two_df.R")
+
+#==========================
+# should return the following dfs, directories and variables
+
+# df with NA:
+# merged_df2
+# merged_df3
+
+# df without NA:
+# merged_df2_comp
+# merged_df3_comp
+
+# my_df_u
+
+cat(paste0("Directories imported:"
+           , "\ndatadir:", datadir
+           , "\nindir:", indir
+           , "\noutdir:", outdir
+           , "\nplotdir:", plotdir))
+
+cat(paste0("Variables imported:"
+           , "\ndrug:", drug
+           , "\ngene:", gene
+           , "\ngene_match:", gene_match
+           , "\nAngstrom symbol:", angstroms_symbol
+           , "\nNo. of cols:", df_ncols
+           , "\nNo. of duplicated muts:", dup_muts_nu
+           , "\nNA count for ORs:", na_count
+           , "\nNA count in df2:", na_count_df2
+           , "\nNA count in df3:", na_count_df3))       
+
+#=========================
+#=======
+# output
+#=======
+# plot 1
+basic_bp_lineage = "basic_lineage_barplot.svg"
+plot_basic_bp_lineage  =  paste0(plotdir,"/", basic_bp_lineage)
+
+#=======================================================================
+#================
+# Data for plots:
+# you need merged_df2, comprehensive one
+# since this has one-many relationship
+# i.e the same SNP can belong to multiple lineages
+#================
+# REASSIGNMENT as necessary
+my_df  = merged_df2
+#my_df  = merged_df2_comp
+
+# clear excess variable
+rm(merged_df2_comp, merged_df3, merged_df3_comp)
+
+# quick checks
+colnames(my_df)
+str(my_df)
+
+# Ensure correct data type in columns to plot: need to be factor
+is.factor(my_df$lineage)
+my_df$lineage = as.factor(my_df$lineage)
+is.factor(my_df$lineage)
+
+#==========================
+# Plot: Lineage barplot
+# x = lineage y = No. of samples
+# col = Lineage
+# fill = lineage
+#============================
+table(my_df$lineage)
+
+#****************
+# Plot: Lineage Barplot
+#****************
+
+#=============
+# Data for plots
+#=============
+
+# REASSIGNMENT
+df <- my_df
+
+rm(my_df)
+
+# get freq count of positions so you can subset freq<1
+#setDT(df)[, lineage_count := .N, by = .(lineage)]
+
+#******************
+# generate plot: barplot of mutation by lineage
+#******************
+sel_lineages = c("lineage1"
+                 , "lineage2"
+                 , "lineage3"
+                 , "lineage4"
+                 #, "lineage5"
+                 #, "lineage6"
+                 #, "lineage7"
+                 )
+
+df_lin = subset(df, subset = lineage %in% sel_lineages )
+
+#FIXME; add sanity check for numbers.
+# Done this manually
+
+############################################################
+
+#########
+# Data for barplot: Lineage barplot
+# to show total samples and number of unique mutations 
+# within each linege
+##########
+
+# Create df with lineage inform & no. of unique mutations
+# per lineage and total samples within lineage
+# this is essentially barplot with two y axis
+
+bar = bar = as.data.frame(sel_lineages) #4, 1
+total_snps_u = NULL
+total_samples = NULL
+
+for (i in sel_lineages){
+  #print(i)
+  curr_total = length(unique(df$id)[df$lineage==i])
+  total_samples = c(total_samples, curr_total)
+  print(total_samples)
+  
+  foo = df[df$lineage==i,]
+  print(paste0(i, "======="))
+  print(length(unique(foo$mutationinformation)))
+  curr_count = length(unique(foo$mutationinformation))
+
+  total_snps_u = c(total_snps_u, curr_count)
+}
+
+print(total_snps_u)
+bar$num_snps_u = total_snps_u
+bar$total_samples = total_samples
+bar
+
+#*****************
+# generate plot: lineage barplot with two y-axis
+#https://stackoverflow.com/questions/13035295/overlay-bar-graphs-in-ggplot2
+#*****************
+
+y1 = bar$num_snps_u
+y2 = bar$total_samples
+x = sel_lineages
+
+to_plot = data.frame(x = x
+                      , y1 = y1
+                      , y2 = y2)
+to_plot
+
+# FIXME later: will be depricated!
+melted = melt(to_plot, id = "x")
+melted
+
+
+svg(plot_basic_bp_lineage)
+
+my_ats = 20 # axis text size
+my_als = 22 # axis label size
+
+g = ggplot(melted, aes(x = x
+                 , y = value
+                 , fill = variable))
+
+printFile = g + geom_bar(stat = "identity"
+                         , position = position_stack(reverse = TRUE)
+                         , alpha=.75
+                         , colour='grey75') + 
+  theme(axis.text.x = element_text(size = my_ats)
+        , axis.text.y = element_text(size = my_ats
+                                     #, angle = 30
+                                     , hjust = 1
+                                     , vjust = 0)
+        , axis.title.x = element_text(size = my_als
+                                      , colour = 'black')
+        , axis.title.y = element_text(size = my_als
+                                      , colour = 'black')
+        , legend.position = "top"
+        , legend.text = element_text(size = my_als) + 
+          #geom_text() +
+          geom_label(aes(label = value)
+                     , size = 5
+                     , hjust = 0.5
+                     , vjust = 0.5
+                     , colour = 'black'
+                     , show.legend = FALSE
+                     #, check_overlap = TRUE
+                     , position = position_stack(reverse = T)) + 
+          labs(title = ''
+               , x = ''
+               , y = "Number"
+               , fill = 'Variable'
+               , colour = 'black') + 
+          scale_fill_manual(values = c('grey50', 'gray75')
+                            , name=''
+                            , labels=c('Mutations', 'Total Samples')) +
+          scale_x_discrete(breaks = c('lineage1', 'lineage2', 'lineage3', 'lineage4')
+                           , labels = c('Lineage 1', 'Lineage 2', 'Lineage 3', 'Lineage 4')))
+
+print(printFile)
+dev.off()