tanu/LSHTM_analysis
1
0
Fork 0
Code Issues Pull requests Releases Wiki Activity

generated pncA plot for poster for ps_combined

Browse source
This commit is contained in:
Tanushree Tunstall 2021-07-07 11:38:07 +01:00
parent cb3a0f71da
commit 59a1213f65
3 changed files with 37 additions and 17 deletions
Download patch file Download diff file Expand all files Collapse all files

14
scripts/plotting/get_plotting_dfs.R
View file

@ -39,10 +39,10 @@ import_dirs(drug, gene)
#---------------------------
# call: plotting_data()
#---------------------------
#if (!exists("infile_params") && exists("gene")){
if (!is.character(infile_params) && exists("gene")){ # when running as cmd
#in_filename_params = paste0(tolower(gene), "_all_params.csv")
in_filename_params = paste0(tolower(gene), "_comb_afor.csv") # part combined for gid
if (!exists("infile_params") && exists("gene")){
#if (!is.character(infile_params) && exists("gene")){ # when running as cmd
in_filename_params = paste0(tolower(gene), "_all_params.csv") #for pncA
#in_filename_params = paste0(tolower(gene), "_comb_afor.csv") # part combined for gid
infile_params = paste0(outdir, "/", in_filename_params)
cat("\nInput file for mcsm comb data not specified, assuming filename: ", infile_params, "\n")
}
@ -62,8 +62,8 @@ dup_muts = pd_df[[4]]
#--------------------------------
# call: combining_dfs_plotting()
#--------------------------------
#if (!exists("infile_metadata") && exists("gene")){
if (!is.character(infile_metadata) && exists("gene")){ # when running as cmd
if (!exists("infile_metadata") && exists("gene")){
#if (!is.character(infile_metadata) && exists("gene")){ # when running as cmd
in_filename_metadata = paste0(tolower(gene), "_metadata.csv") # part combined for gid
infile_metadata = paste0(outdir, "/", in_filename_metadata)
cat("\nInput file for gene metadata not specified, assuming filename: ", infile_metadata, "\n")
@ -102,7 +102,7 @@ cols_to_select = c("mutationinformation", "drtype"
, "duet_stability_change", "duet_outcome", "duet_scaled"
, "ligand_affinity_change", "ligand_outcome", "affinity_scaled"
, "ddg", "foldx_scaled", "foldx_outcome"
, "deepddg", "deepddg_outcome"
#, "deepddg", "deepddg_outcome"
, "asa", "rsa", "rd_values", "kd_values"
, "af", "or_mychisq", "pval_fisher"
, "or_fisher", "or_logistic", "pval_logistic"

31
scripts/plotting/ps_plots_combined.R
View file

@ -7,14 +7,15 @@
# Installing and loading required packages
##########################################################
getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting/")
setwd("~/git/LSHTM_analysis/scripts/plotting")
getwd()
source("Header_TT.R")
library(ggplot2)
library(data.table)
#source("combining_dfs_plotting.R")
source("../functions/bp_subcolours.R")
#source("../functions/bp_subcolours.R")
source("get_plotting_dfs.R")
source("subcols_axis.R")
###########################
@ -199,7 +200,7 @@ p1 = g1 +
labs(title = ""
#, size = 100
#, x = "Wild-type position"
, y = "AF(%)")
, y = "MAF(%)")
p1
#=================
@ -239,7 +240,7 @@ p2
#============================
# combined plot 1: UNlabelled
#============================
ps_combined = "af_or_combined_PS.svg"
ps_combined = "af_or_combined_PS_v2.svg"
plot_ps_combined = paste0(plotdir,"/", ps_combined)
cat("combined plot Unlabelled:", plot_ps_combined)
@ -253,7 +254,7 @@ dev.off()
#============================
# combined plot 2: labelled
#============================
ps_combined_labelled = "af_or_combined_PS_labelled.svg"
ps_combined_labelled = "af_or_combined_PS_labelled_v2.svg"
plot_ps_combined_labelled = paste0(plotdir,"/", ps_combined_labelled)
cat("combined plot Labelled:", plot_ps_combined_labelled)
@ -267,3 +268,23 @@ OutPlot_combined_labelled = cowplot::plot_grid(p1, p2, p3
, hjust = -0.4)
OutPlot_combined_labelled
dev.off()
#============================
# combined plot 2: labelled
# ISMB poster July 2021
#============================
ps_combined_labelled_poster = "af_or_combined_PS_labelled_v2_poster.svg"
plot_ps_combined_labelled_poster = paste0(plotdir,"/", ps_combined_labelled_poster)
cat("combined plot Labelled:", plot_ps_combined_labelled_poster)
svg(plot_ps_combined_labelled_poster , width = 26, height = 8)
OutPlot_combined_labelled_poster = cowplot::plot_grid(p2, p3
, ncol = 1
#, labels = c("(a)", "(b)", "(c)")
, labels = "AUTO"
, label_size = 25
, align = 'hv'
, hjust = -0.4)
OutPlot_combined_labelled_poster
dev.off()

9
scripts/plotting/subcols_axis.R
View file

@ -7,7 +7,7 @@ getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting")
getwd()
source("plotting_data.R")
#source("get_plotting_data.R")
# should return the following dfs and directories
# my_df
# my_df_u
@ -24,11 +24,11 @@ cat(paste0("Variables imported:"
, "\ndrug:", drug
, "\ngene:", gene
, "\ngene_match:", gene_match
, "\nLength of upos:", length(upos)
#, "\nLength of upos:", length(upos)
, "\nAngstrom symbol:", angstroms_symbol))
# clear excess variable
rm(upos, dup_muts, my_df_u, my_df_u_lig)
#rm(upos, dup_muts, my_df_u, my_df_u_lig)
# This is because we want to assign the colours to my_df
# and then resubset accordingly for our plots to avoid multiple merges
@ -237,5 +237,4 @@ rm(aa_cols_ref
#######################################################################
# end of script
#######################################################################
#######################################################################