196 lines
No EOL
6.4 KiB
R
196 lines
No EOL
6.4 KiB
R
library(tidyverse)
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library("ggforce")
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library(gginference)
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library(ggpubr)
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library(svglite)
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# for testing only
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#gene="pncA"
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#drug="pyrazinamide"
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lineage_plot=function(gene,drug){
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lineage_filename=paste0(tolower(gene),"_merged_df2.csv")
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lineage_data_path=paste0("~/git/Data/", drug, "/output") # NARSTY
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full_file_path = paste0(lineage_data_path,"/",lineage_filename)
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print(paste0("Loading: ",full_file_path))
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df = read.csv(full_file_path)
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#df2 = read.csv("~/git/Data/pyrazinamide/output/pnca_merged_df3.csv")
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foo = as.data.frame(colnames(df))
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cols_to_subset = c('mutationinformation'
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, 'snp_frequency'
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, 'pos_count'
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, 'position'
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, 'lineage'
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, 'lineage_multimode'
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, 'dst'
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, 'dst_multimode'
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#, 'dst_multimode_all'
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, 'dst_mode')
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my_df = df[ ,cols_to_subset]
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#df2 = df2[ ,cols_to_subset]
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# Now we need to make a column that fill na in dst with value of dst_mode
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my_df$dst2 = ifelse(is.na(my_df$dst), my_df$dst_mode, my_df$dst)
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#%% create sensitivity column ~ dst_mode
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my_df$sensitivity = ifelse(my_df$dst2 == 1, "R", "S")
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table(my_df$dst2)
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if ( table(my_df$sensitivity)[2] == table(my_df$dst2)[1] && table(my_df$sensitivity)[1] == table(my_df$dst2)[2] ){
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cat("\nProceeding with lineage resistance plots")
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}else{
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stop("FAIL: could not verify dst2 and sensitivity numbers")
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}
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#%%
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# select only L1-L4 and LBOV
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sel_lineages1 = c("LBOV", "")
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my_df2 = my_df[!my_df$lineage%in%sel_lineages1,]
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table(my_df2$lineage)
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sel_lineages2 = c("L1", "L2", "L3", "L4")
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my_df2 = my_df2[my_df2$lineage%in%sel_lineages2,]
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table(my_df2$lineage)
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sum(table(my_df2$lineage)) == nrow(my_df2)
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table(my_df2$lineage)
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#%% get only muts which belong to > 1 lineage and have different sensitivity classifications
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muts = unique(my_df2$mutationinformation)
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# step1 : get muts with more than one lineage
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lin_muts = NULL
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for (i in muts) {
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print (i)
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s_mut = my_df2[my_df2$mutationinformation == i,]
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s_tab = table(s_mut$lineage, s_mut$sensitivity)
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#print(s_tab)
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if (dim(s_tab)[1] > 1 && dim(s_tab)[2] > 1){
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lin_muts = c(lin_muts, i)
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}
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}
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cat("\nGot:", length(lin_muts), "mutations belonging to >1 lineage with differing drug sensitivities")
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# step 2: subset these muts for plotting
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plot_df = my_df2[my_df2$mutationinformation%in%lin_muts,]
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cat("\nnrow of plot_df:", nrow(plot_df))
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# step 3: Add p-value
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plot_df$pval = NULL
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for (i in lin_muts) {
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#print (i)
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s_mut = plot_df[plot_df$mutationinformation == i,]
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s_tab = table(s_mut$lineage, s_mut$sensitivity)
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ft_pvalue_i = fisher.test(s_tab, workspace=2000000)$p.value
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plot_df$pval[plot_df$mutationinformation == i] <- ft_pvalue_i
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}
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plot_df$pvalR = round(plot_df$pval, 3)
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plot_df$pvalRF = ifelse(plot_df$pvalR == 0.05, paste0("p=",plot_df$pvalR, "."), plot_df$pvalR )
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plot_df$pvalRF = ifelse(plot_df$pvalR <= 0.05, paste0("p=",plot_df$pvalR, "*"), plot_df$pvalRF )
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plot_df$pvalRF = ifelse(plot_df$pvalR <= 0.01, paste0("p=",plot_df$pvalR, "**"), plot_df$pvalRF )
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plot_df$pvalRF = ifelse(plot_df$pvalR == 0, 'p<0.001, ***', plot_df$pvalRF)
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plot_df$pvalRF = ifelse(plot_df$pvalR > 0.05, paste0("p=",plot_df$pvalR), plot_df$pvalRF)
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# format p value
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lin_muts_tb = plot_df %>%
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group_by(mutationinformation) %>%
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count(lineage) %>%
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mutate(ypos_label = max(n))
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head(lin_muts_tb); class(lin_muts_tb)
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lin_muts_df = as.data.frame(lin_muts_tb)
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class(lin_muts_df)
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intersect(names(plot_df), names(lin_muts_df))
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select_cols = c("mutationinformation", "ypos_label")
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lin_muts_df2 = lin_muts_df[, select_cols]
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names(lin_muts_df2) ; head(lin_muts_df2)
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# remove duplicates before merging
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lin_muts_df2U = lin_muts_df2[!duplicated(lin_muts_df2),]
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class(lin_muts_df2); class(plot_df); class(lin_muts_df2U)
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lin_muts_dfM = merge(plot_df, lin_muts_df2U, by = "mutationinformation", all.y = T)
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if (nrow(lin_muts_dfM) == nrow(plot_df) ){
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cat("\nPASS: plot_df now has ypos for label"
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, "\nGenerating plot_df2 with sensitivity as factor\n")
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str(lin_muts_dfM)
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lin_muts_dfM$sensitivity = as.factor(lin_muts_dfM$sensitivity)
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plot_df2 = lin_muts_dfM
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}else{
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stop("\nSomething went wrong. ypos_label could not be generated")
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}
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# Do plots
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plot_pages = round(length(lin_muts)/25)
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if (plot_pages<1){plot_pages=1}
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p_title = gene
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res = 144 # SVG dots-per-inch
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print(paste0('About to plot ', plot_pages, ' page(s).'))
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sapply(1:plot_pages, function(page){
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print(paste0("Plotting page:", page))
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svglite(paste0("/tmp/",drug,"-",page,".svg"), width=2048/res, height=1534/res) # old-school square 4:3 CRT shape 1.33:1
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print(
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ggplot(plot_df2, aes(x = lineage
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, fill = sensitivity)) +
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geom_bar(stat = 'count') +
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facet_wrap_paginate(~mutationinformation
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, scales = 'free_y'
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, ncol = 5
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, nrow = 5
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, page = page) +
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theme(legend.position = "top"
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, plot.title = element_text(hjust = 0.5, size=20)
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, strip.text = element_text(size=14)
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, axis.text.x = element_text(size=14)
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, axis.text.y = element_text(size=14)
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, axis.title.y = element_text(size=14)
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, legend.title = element_blank()
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, axis.title.x = element_blank()
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)+
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labs(title = paste0(p_title, ": sensitivity by lineage")
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, y = 'Sample Count'
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) +
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#geom_text(aes(label = p.value, x = 0.5, y = 5))
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geom_blank(aes(y = ypos_label+1.25)) +
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geom_label(aes(label = pvalRF, x = 2.5, ypos_label+0.75), fill="white")
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)
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dev.off()
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}
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)
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}
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# hardcoded list of drugs
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drugs = c(#"ethambutol",
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"isoniazid",
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"pyrazinamide",
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"rifampicin",
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"streptomycin",
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#"cycloserine"
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)
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genes = c(#"embB",
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"katG",
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"pncA",
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"rpoB",
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"gid",
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#"alr"
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)
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combo = data.frame(drugs, genes)
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#sapply(combo$drugs, function(x){print(c(x,combo[drugs==x,"genes"]))})
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# generate graphs for all drug/gene combinations in "combo"
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sapply(combo$drugs, function(drug){
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gene=combo[drugs==drug,"genes"]
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lineage_plot(gene,drug)
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print(c(gene,drug))
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}) |