added hist_af.R
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378
scripts/plotting/hist_af.R
Executable file
378
scripts/plotting/hist_af.R
Executable file
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#!/usr/bin/env Rscript
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#########################################################
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# TASK: producing histogram of AF
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# basic
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# basic
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#########################################################
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#=======================================================================
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# working dir and loading libraries
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getwd()
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setwd("~/git/LSHTM_analysis/scripts/plotting")
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getwd()
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#source("Header_TT.R")
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library(ggplot2)
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library(data.table)
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library(dplyr)
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library(plyr)
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#source("plotting_data.R")
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source("combining_dfs_plotting.R")
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# clear excess variable
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rm(my_df, upos, dup_muts, my_df_u_lig)
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#=======================================================================
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#=======
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# output
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#=======
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# plot 1
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hist_af_muts = "hist_af_mutations.svg"
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plot_hist_af_muts = paste0(plotdir,"/", hist_af_muts)
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# plot 2
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hist_af_samples = "hist_af_samples.svg"
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plot_hist_af_samples = paste0(plotdir, "/", hist_af_samples )
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#=======================================================================
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merged_df3_comp$mutation_info_labels = ifelse(merged_df3_comp$mutation_info == dr_muts_col, "DM", "OM")
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table(merged_df3_comp$mutation_info_labels)
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table(merged_df3_comp$mutation_info) == table(merged_df3_comp$mutation_info_labels)
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merged_df2_comp$mutation_info_labels = ifelse(merged_df2_comp$mutation_info == dr_muts_col, "DM", "OM")
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table(merged_df2_comp$mutation_info_labels)
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table(merged_df2_comp$mutation_info) == table(merged_df2_comp$mutation_info_labels)
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#================
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# Data for plots
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#================
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# REASSIGNMENT as necessary
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df = my_df_u
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df3 = merged_df3_comp
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# Contains duplicated samples, so you need to remove that for AF hist
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merged_df2_comp_u = merged_df2_comp[!duplicated(merged_df2_comp$id),]
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if ( nrow(merged_df2_comp_u) == length(unique(merged_df2_comp$id)) ){
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cat("PASS: duplicated samples ommitted. Assiging for plotting...")
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df2 = merged_df2_comp_u
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}else{
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cat("FAIL: duplicated samples could not be ommitted. Length mismatch"
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, "Expected nrows:", length(unique(merged_df2_comp$id))
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, "Got nrows:", nrow(merged_df2_comp_u))
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}
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df2_af_median <- ddply(df2, "mutation_info_labels", summarise, grp.median = median(af, na.rm = T))
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head(df2_af_median)
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#=======================================================================
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#****************
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# Plot 1: AF distribution: mutations
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#****************
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svg(plot_hist_af_muts)
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print(paste0("plot1 filename:", plot_hist_af_muts))
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#--------------
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# start plot 1
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#--------------
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#par(mar=c(b, l, t, r))
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par(mar=c(5,6,1.3,0))
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h1 = hist(df3$af
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, freq = T
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, breaks = 30
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, xlab = "Minor Allele Frequency"
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, ylab = "Frequency"
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, main = ""
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, cex.lab = 1.7
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, cex.axis = 1.5
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, cex.main = 1.5
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, cex.sub = 1.5)
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print(h1)
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dev.off()
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#****************
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# Plot 2: AF distribution: samples
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#****************
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svg(plot_hist_af_samples)
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print(paste0("plot2 filename:", plot_hist_af_samples))
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#--------------
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# start plot 1
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#--------------
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#par(mar=c(b, l, t, r))
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par(mar=c(5,6,1,0))
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h2 = hist(df2$af
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, freq = T
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, breaks = 30
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, xlab = "Minor Allele Frequency"
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, ylab = "Frequency"
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, main = ""
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, cex.lab = 1.7
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, cex.axis = 1.5
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, cex.main = 1.5
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, cex.sub = 1.5)
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print(h2)
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dev.off()
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#=====================================================================
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hist(df3$af
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, freq = T
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, breaks = 30
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, xlab = "Minor Allele Frequency"
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, ylab = "Frequency"
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, main = ""
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, cex.lab = 1.7
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, cex.axis = 1.5
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, cex.main = 1.5
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, cex.sub = 1.5)
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hist(df3$af[df3$mutation_info_labels == "DM"]
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, col = "#E69F00"
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, breaks = 30
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#, add = T
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, freq = T
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, xlab = "Minor Allele Frequency"
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, ylab = "Frequency"
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, main = ""
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, cex.lab = 1.7
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, cex.axis = 1.5
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, cex.main = 1.5
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, cex.sub = 1.5)
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######################################################################################
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#############
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# ggplots
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#############
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#library(plyr)
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df3_af_median <- ddply(df3, "mutation_info_labels", summarise, grp.median = median(af, na.rm = T))
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head(df3_af_median)
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my_ats = 15 # axis text size
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my_als = 18 # axis label size
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theme_set(theme_grey())
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g_af_hist = ggplot(df3, aes(x = af)) +
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geom_histogram(colour = "white") +
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theme(axis.text.x = element_text(size = my_ats)
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, axis.text.y = element_text(size = my_ats)
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#, axis.title.y = element_blank()
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, axis.title.x = element_text(size = my_ats)
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#, axis.title.x = element_blank()
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, axis.title.y = element_text(size = my_ats)
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, axis.ticks.y = element_blank()
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, plot.title = element_blank())+
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labs(y = "Count"
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, x = "Minor Allele Frequency"
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)
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g_af_hist
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#=====================================================================
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df3_af_median <- ddply(df3, "mutation_info_labels", summarise, grp.median = median(af, na.rm = T))
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head(df3_af_median)
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g_af_hist_col = ggplot(df3, aes(x = af, fill = mutation_info_labels)) +
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geom_histogram(position = "stack") +
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scale_fill_manual(values = c("#E69F00", "#999999")) +
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theme(axis.text.x = element_text(size = my_ats)
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, axis.text.y = element_text(size = my_ats)
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#, axis.title.y = element_blank()
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, axis.title.x = element_text(size = my_ats)
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#, axis.title.x = element_blank()
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, axis.title.y = element_text(size = my_ats)
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, axis.ticks.y = element_blank()
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, plot.title = element_blank())+
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labs(y = "Count"
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, x = "Minor Allele Frequency"
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)
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g_af_hist_col
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g_af_hist_col_med = g_af_hist_col + geom_vline(data = df3_af_median, aes(xintercept = grp.median),
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linetype = "dashed")
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g_af_hist_col_med
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#=====================================================================
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g_af_mutinfo = ggplot(df3, aes(x = af
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, fill = mutation_info_labels)) +
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scale_fill_manual(values = c("#E69F00", "#999999")) +
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geom_histogram() +
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facet_grid(mutation_info_labels ~ ., scales = "free") +
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#facet_wrap(mutation_info_labels ~ ., scales = "free") +
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theme(axis.text.x = element_text(size = my_ats)
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, axis.text.y = element_text(size = my_ats)
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, axis.title.x = element_text(size = my_ats)
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#, axis.title.y = element_blank()
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, axis.title.y = element_text(size = my_ats)
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, axis.ticks.y = element_blank()
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, plot.title = element_blank()
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, strip.text = element_text(size = my_als)
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, legend.text = element_text(size = my_als-4)
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, legend.title = element_text(size = my_als-4)
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, legend.position = c(0.8, 0.9)) +
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labs(x = "Minor Allele Frequency (MAF)"
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, y = "Count"
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, fill = "Mutation class")
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g_af_mutinfo
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g_af_mutinfo_med = g_af_mutinfo + geom_vline(data = df3_af_median, aes(xintercept = grp.median),
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linetype = "dashed")
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g_af_mutinfo_med
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#=====================================================================
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g_af_bp = ggplot(df3, aes(x = mutation_info_labels
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, y = af
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, fill = mutation_info_labels))+
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scale_fill_manual(values = c("#E69F00", "#999999")) +
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geom_boxplot()+
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theme(axis.text.x = element_text(size = my_ats)
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, axis.text.y = element_text(size = my_ats)
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, axis.title.x = element_text(size = my_ats)
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#, axis.title.y = element_blank()
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, axis.title.y = element_text(size = my_ats)
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, axis.ticks.y = element_blank()
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, plot.title = element_blank()
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, strip.text = element_text(size = my_als)
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, legend.text = element_text(size = my_als-4)
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, legend.title = element_text(size = my_als-4)
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, legend.position = c(0.8, 0.9)) +
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labs(y = "Minor Allele Frequency (MAF)"
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, x = ""
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, fill = "Mutation class")
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g_af_bp
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#=====================================================================
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###################
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# combine: afs
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###################
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library(cowplot)
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grid.arrange(g_af_hist, g_af_mutinfo, g_af_bp)
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c2 = cowplot::plot_grid(g_mutinfo, g_bp
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, nrow = 2
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, labels = c("(a)", "(b)")
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, rel_widths = c(1.5/2, 0.25/2)
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, label_size = 20)
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print(c2)
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######################################################################
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# OR
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######################################################################
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df3_or_median <- ddply(df3, "mutation_info_labels", summarise, grp.median = median(or_mychisq, na.rm = T))
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head(df3_or_median)
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g_or_mutinfo = ggplot(df3, aes(x = or_mychisq
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, fill = mutation_info_labels)) +
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scale_fill_manual(values = c("#E69F00", "#999999")) +
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geom_histogram() +
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facet_grid(mutation_info_labels ~ ., scales = "free") +
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#facet_wrap(mutation_info_labels ~ ., scales = "free") +
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theme(axis.text.x = element_text(size = my_ats)
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, axis.text.y = element_text(size = my_ats)
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, axis.title.x = element_text(size = my_ats)
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, axis.title.y = element_text(size = my_ats)
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#, axis.title.y = element_blank()
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, axis.ticks.y = element_blank()
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, plot.title = element_blank()
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, strip.text = element_text(size = my_als)
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, legend.text = element_text(size = my_als-4)
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, legend.title = element_text(size = my_als-4)
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, legend.position = c(0.8, 0.9)) +
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labs(x = "Odds Ratio"
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, y = "Count"
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, fill = "Mutation class")
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g_or_mutinfo
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g_or_mutinfo_med = g_or + geom_vline(data = df3_or_median, aes(xintercept = grp.median),
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linetype = "dashed")
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g_or_mutinfo_med
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#=====================================================================
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g_or_bp = ggplot(df3, aes(x = mutation_info_labels
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, y = or_mychisq
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, fill = mutation_info_labels))+
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scale_fill_manual(values = c("#E69F00", "#999999")) +
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geom_boxplot()+
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theme(axis.text.x = element_text(size = my_ats)
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, axis.text.y = element_text(size = my_ats)
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, axis.title.x = element_text(size = my_ats)
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#, axis.title.y = element_blank()
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, axis.title.y = element_text(size = my_ats)
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, axis.ticks.y = element_blank()
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, plot.title = element_blank()
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, strip.text = element_text(size = my_als)
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, legend.text = element_text(size = my_als-4)
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, legend.title = element_text(size = my_als-4)
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, legend.position = c(0.8, 0.9)) +
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labs(y = "Odds Ratio"
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, x = ""
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, fill = "Mutation class")
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g_or_bp
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###################
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# combine: afs
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###################
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library(cowplot)
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c_or = cowplot::plot_grid(g_or_mutinfo, g_or_bp
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, nrow = 2
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, labels = c("(a)", "(b)")
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, rel_widths = c(1.5/2, 0.25/2)
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, label_size = 20)
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print(c_or)
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c_combined = cowplot::plot_grid(g_af_mutinfo
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, g_af_bp
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, g_or_mutinfo
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, g_or_bp
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, nrow = 2
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, labels = c("(a)", "(b)", "(c)", "(d)")
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, rel_widths = c(2/3, 1/3)
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, label_size = 20)
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print(c_combined)
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c_combined2 = cowplot::plot_grid(g_af_mutinfo
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, g_or_mutinfo
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, g_af_bp
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, g_or_bp
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, nrow = 2
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, labels = c("(a)", "(b)", "(c)", "(d)")
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#, rel_widths = c(1.5/2, 0.25/2)
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, label_size = 20)
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#print(c_combined2)
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######################################################################
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########################################################################
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# end of hist AF
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########################################################################
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par(mfrow=c(1,2))
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hist(df2$af
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, xlab = "Minor Allele Frequency"
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, ylab = "Frequency"
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, main = paste0(nrow(df2),"_pnca_samples"))
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hist(df3$af
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, freq = T
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, xlab = "Minor Allele Frequency"
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, ylab = "Frequency"
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, main = paste0(nrow(df3),"_pnca_mutations"))
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