added base histogram script for af and or
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scripts/plotting/hist_af_or_base.R
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scripts/plotting/hist_af_or_base.R
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#!/usr/bin/env Rscript
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#########################################################
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# TASK: producing histogram of AF and OR
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# output svgs
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# 1) hist of af
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# 2) hist of or
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# 3) hist of af_or combined
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# 4) hist of af: from muts and samples dfs combined (EXPLORATORY!)
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# 5) hist and barplots for af_or combined with median line
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# 6) hist and barplots for af_or combined withOUT median line (Turned OFF)
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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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#=======================================================================
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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_mutations_AF.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_or_muts = "hist_mutations_OR.svg"
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plot_hist_or_muts = paste0(plotdir,"/", hist_or_muts)
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# plot 3
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hist_af_muts_sample = "hist_af_muts_sample_combined.svg"
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plot_hist_af_muts_sample = paste0(plotdir,"/", hist_af_muts_sample)
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# plot 4
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hist_af_or = "hist_af_or_combined.svg"
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plot_hist_af_or = paste0(plotdir,"/", hist_af_or)
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# plot 5
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af_or_combined_med = "hist_bp_muts_combined_median.svg"
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plot_af_or_combined_med = paste0(plotdir, "/", af_or_combined_med)
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# plot 6: without median line on hist
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af_or_combined = "hist_bp_muts_combined.svg"
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plot_af_or_combined = paste0(plotdir, "/", af_or_combined)
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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$mutation_info_labels)
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sum(table(merged_df3_comp$mutation_info))
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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$mutation_info_labels)
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sum(table(merged_df2_comp$mutation_info))
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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$id))
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, "Got nrows:", nrow(merged_df2_comp_u))
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}
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#=======================================================================
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#****************
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# Plot 1: AF distribution: mutations
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#****************
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svg(plot_hist_af_muts)
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print(paste0("plot1 filename:", plot_hist_af_muts))
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#par(mar=c(b, l, t, r))
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par(mar = c(4.5, 6, 1.8, 0))
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hist(df3$af
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, freq = T
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, breaks = 30
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, xlab = "MAF"
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, ylab = "Frequency"
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, main = "Minor Allele Frequency (MAF)"
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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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dev.off()
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#****************
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# Plot 2: AF distribution: samples
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#****************
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par(mar = c(4.5, 6, 1.8, 0))
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hist(df2$af
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, freq = T
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, breaks = 30
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, xlab = "MAF"
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, ylab = "Frequency"
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, main = "Minor Allele Frequency (MAF)"
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, cex.lab = 1.7
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, cex.lab = 1.7
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, cex.axis = 1.5
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, cex.main = 1.5
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, cex.sub = 1.5)
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#****************
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# Plot 3: OF distribution: mutations
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#****************
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svg(plot_hist_or_muts)
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print(paste0("plot3 filename:", plot_hist_or_muts))
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par(mar = c(4.5, 6, 1.8, 0))
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hist(df3$or_mychisq
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, freq = T
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, breaks = 30
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, xlab = "OR"
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, ylab = "Frequency"
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, main = "Odds Ratio (OR)"
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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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dev.off()
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#====================================================================
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#==========
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# combine and output
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#==========
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#--------------
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# combine: af and or
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#-------------
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svg(plot_hist_af_or, width = 10, height = 8)
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print(paste0("plot3 filename:", plot_hist_af_or))
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par(mfrow = c(1,2))
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par(mar = c(4.5, 5.5, 2, 0))
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hist(df3$af
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, freq = T
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, breaks = 30
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, xlab = "Minor Allele Frequency (MAF)"
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, ylab = "Frequency"
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, main = ""
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, cex.lab = 1.3
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, cex.axis = 1.3
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, cex.main = 1.5
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, cex.sub = 1.5)
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# print the overall labels
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mtext(expression(bold('(a)')), side = 3, adj = -0.1, cex = 1.8)
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hist(df3$or_mychisq
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, freq = T
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, breaks = 30
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, xlab = "Odds Ratio (OR)"
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, ylab = "Frequency"
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, main = ""
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, cex.lab = 1.3
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, cex.axis = 1.3
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, cex.main = 1.5
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, cex.sub = 1.5)
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# print the overall labels
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mtext(expression(bold('(b)')), side = 3, adj = -0.1, cex = 1.8)
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dev.off()
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#--------------
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# combine: af (mutations and samples)
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#-------------
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svg(plot_hist_af_muts_sample, width = 10, height = 8)
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print(paste0("plot3 filename:", plot_hist_af_muts_sample))
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par(mfrow = c(1,2))
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par(mar = c(4.5, 5.5, 2, 0))
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hist(df3$af
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, freq = T
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, breaks = 30
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, xlab = "Minor Allele Frequency (MAF)"
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, ylab = "Frequency"
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, main = paste0(nrow(df3),"_pnca_mutations")
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, cex.lab = 1.3
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, cex.axis = 1.3
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, cex.main = 1.5
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, cex.sub = 1.5)
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hist(df2$af
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, freq = T
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, breaks = 30
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, xlab = "Minor Allele Frequency (MAF)"
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, ylab = "Frequency"
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, main = paste0(nrow(df2),"_pnca_samples")
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, cex.lab = 1.3
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, cex.axis = 1.3
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, cex.main = 1.5
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, cex.sub = 1.5)
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dev.off()
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########################################################
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