generated pncA plot for poster for ps_combined

scripts/plotting/get_plotting_dfs.R

@@ -39,10 +39,10 @@ import_dirs(drug, gene)
 #---------------------------
 # call: plotting_data()
 #---------------------------
-#if (!exists("infile_params") && exists("gene")){
+if (!exists("infile_params") && exists("gene")){
-if (!is.character(infile_params) && exists("gene")){ # when running as cmd
+#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), "_all_params.csv") #for pncA
-  in_filename_params = paste0(tolower(gene), "_comb_afor.csv") # part combined for gid
+  #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 (!exists("infile_metadata") && exists("gene")){
-if (!is.character(infile_metadata) && exists("gene")){ # when running as cmd
+#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"

scripts/plotting/ps_plots_combined.R

@@ -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()

scripts/plotting/subcols_axis.R

@@ -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
-#######################################################################
+#######################################################################
-