import commit

mcsm_analysis/pyrazinamide/scripts/plotting/lineage_basic_barplot.R

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+getwd()
+setwd("~/git/LSHTM_analysis/mcsm_analysis/pyrazinamide/scripts/plotting") 
+getwd()
+
+########################################################################
+# 				Installing and loading required packages 			   #
+########################################################################
+
+source("../Header_TT.R")
+#source("barplot_colour_function.R")
+
+require(data.table)
+
+########################################################################
+#		 Read file: call script for combining df		   	  		   #
+########################################################################
+
+source("../combining_two_df.R")
+
+#---------------------- PAY ATTENTION
+# the above changes the working dir
+#[1] "git/LSHTM_analysis/mcsm_analysis/pyrazinamide/scripts"
+#---------------------- PAY ATTENTION
+
+#==========================
+# This will return:
+
+# df with NA:
+# merged_df2
+# merged_df3
+
+# df without NA:
+# merged_df2_comp
+# merged_df3_comp
+#==========================
+
+###########################
+# 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
+###########################
+
+# uncomment as necessary
+#<<<<<<<<<<<<<<<<<<<<<<<<<
+# REASSIGNMENT
+my_df  = merged_df2
+#my_df  = merged_df2_comp
+#<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# delete variables not required
+rm(merged_df2, 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$lineage)
+
+#        lineage1   lineage2   lineage3   lineage4   lineage5   lineage6 lineageBOV 
+#3        104       1293        264       1311          6          6        105 
+
+#===========================
+# Plot: Lineage Barplots
+#===========================
+
+#===================
+# Data for plots
+#===================
+
+#<<<<<<<<<<<<<<<<<<<<<<<<<
+# REASSIGNMENT
+df <- my_df
+#<<<<<<<<<<<<<<<<<<<<<<<<<
+rm(my_df)
+
+# get freq count of positions so you can subset freq<1
+#setDT(df)[, lineage_count := .N, by = .(lineage)]
+
+#******************
+# generate plot: barplot of mutation by lineage
+#******************
+sel_lineages = c("lineage1"
+                 , "lineage2"
+                 , "lineage3"
+                 , "lineage4")
+
+df_lin = subset(df, subset = lineage %in% sel_lineages )
+
+#FIXME; add sanity check for numbers.
+# Done this manually
+
+############################################################
+
+#########
+# Data for barplot: Lineage barplot
+# to show total samples and number of unique mutations 
+# within each linege
+##########
+
+# Create df with lineage inform & no. of unique mutations
+# per lineage and total samples within lineage
+# this is essentially barplot with two y axis
+
+bar = bar = as.data.frame(sel_lineages) #4, 1
+total_snps_u = NULL
+total_samples = NULL
+
+for (i in sel_lineages){
+  #print(i)
+  curr_total = length(unique(df$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
+#*****************
+
+bar$num_snps_u = y1
+bar$total_samples = y2
+sel_lineages = x
+
+to_plot = data.frame(x = x
+                      , y1 = y1
+                      , y2 = y2)
+to_plot
+
+melted = melt(to_plot, id = "x")
+melted
+
+# set output dir for plots
+getwd()
+setwd("~/git/Data/pyrazinamide/output/plots")
+getwd()
+
+svg('lineage_basic_barplot.svg')
+
+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(
+  
+#g + geom_bar(
+  stat = "identity"
+  , position = position_stack(reverse = TRUE)
+  , alpha=.75
+  , colour='grey75'
+    ) + theme(
+    axis.text.x = element_text(
+      size = my_ats
+#      , angle= 30
+    )
+  , 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)
+    #, position = ('
+
+  ) + 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()