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added ligand df in plotting

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This commit is contained in:
Tanushree Tunstall 2020-08-26 10:02:44 +01:00
parent 73877942f4
commit b754f26f9b
2 changed files with 23 additions and 8 deletions
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7
scripts/plotting/basic_barplots_PS.R
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@ -23,18 +23,19 @@ source("plotting_data.R")
cat(paste0("Directories imported:" cat(paste0("Directories imported:"
, "\ndatadir:", datadir , "\ndatadir:", datadir
, "\nindir:", indir , "\nindir:", indir
, "\noutdir:", outdir)) , "\noutdir:", outdir
, "\nplotdir:", plotdir))
#======= #=======
# output # output
#======= #=======
# plot 1 # plot 1
basic_bp_duet = "basic_barplot_PS.svg" basic_bp_duet = "basic_barplot_PS.svg"
plot_basic_bp_duet = paste0(outdir, "/plots/", basic_bp_duet) plot_basic_bp_duet = paste0(plotdir,"/", basic_bp_duet)
# plot 2 # plot 2
pos_count_duet = "position_count_PS.svg" pos_count_duet = "position_count_PS.svg"
plot_pos_count_duet = paste0(outdir, "/plots/", pos_count_duet) plot_pos_count_duet = paste0(plotdir, "/", pos_count_duet)
#%%=============================================================== #%%===============================================================
#================ #================

24
scripts/plotting/plotting_data.R
View file

@ -39,7 +39,7 @@ cat(gene_match)
datadir = paste0("~/git/Data") datadir = paste0("~/git/Data")
indir = paste0(datadir, "/", drug, "/input") indir = paste0(datadir, "/", drug, "/input")
outdir = paste0("~/git/Data", "/", drug, "/output") outdir = paste0("~/git/Data", "/", drug, "/output")
plotdir = paste0("~/git/Data", "/", drug, "/output/plots")
#====== #======
# input # input
#====== #======
@ -56,15 +56,19 @@ cat("Reading struct params including mcsm:", in_filename_params)
my_df = read.csv(infile_params, header = T) my_df = read.csv(infile_params, header = T)
cat("Input dimensions:", dim(my_df)) cat("\nInput dimensions:", dim(my_df))
# quick checks # quick checks
#colnames(my_df) #colnames(my_df)
#str(my_df) #str(my_df)
###########################
# extract unique mutations
###########################
# check for duplicate mutations # check for duplicate mutations
if ( length(unique(my_df$mutationinformation)) != length(my_df$mutationinformation)){ if ( length(unique(my_df$mutationinformation)) != length(my_df$mutationinformation)){
cat(paste0("CAUTION:", " Duplicate mutations identified" cat(paste0("\nCAUTION:", " Duplicate mutations identified"
, "\nExtracting these...")) , "\nExtracting these..."))
dup_muts = my_df[duplicated(my_df$mutationinformation),] dup_muts = my_df[duplicated(my_df$mutationinformation),]
dup_muts_nu = length(unique(dup_muts$mutationinformation)) dup_muts_nu = length(unique(dup_muts$mutationinformation))
@ -73,14 +77,24 @@ if ( length(unique(my_df$mutationinformation)) != length(my_df$mutationinformati
, "\n\nExtracting df with unique mutations only")) , "\n\nExtracting df with unique mutations only"))
my_df_u = my_df[!duplicated(my_df$mutationinformation),] my_df_u = my_df[!duplicated(my_df$mutationinformation),]
}else{ }else{
cat(paste0("No duplicate mutations detected")) cat(paste0("\nNo duplicate mutations detected"))
my_df_u = my_df my_df_u = my_df
} }
upos = unique(my_df_u$position) upos = unique(my_df_u$position)
cat("Dim of clean df:"); cat(dim(my_df_u)) cat("\nDim of clean df:"); cat(dim(my_df_u))
cat("\nNo. of unique mutational positions:"); cat(length(upos), "\n") cat("\nNo. of unique mutational positions:"); cat(length(upos), "\n")
###########################
# extract mutations <10Angstroms
###########################
table(my_df_u$ligand_distance<10)
my_df_u_lig = my_df_u[my_df_u$ligand_distance <10,]
angstroms_symbol = "\u212b"
cat(paste0("There are ", nrow(my_df_u_lig), " sites lying within 10", angstroms_symbol, " of the ligand"))
######################################################################## ########################################################################
# end of data extraction and cleaning for plots # # end of data extraction and cleaning for plots #
######################################################################## ########################################################################