moved dm_om_data.R the script version to redundant and the function version has been trimmed to for readability

scripts/plotting/dm_om_data.R

@@ -1,62 +0,0 @@
-#!/usr/bin/env Rscript  
-#########################################################
-# TASK: Script to format data for dm om plots: 
-# generating WF LF data
-# sourced by get_plotting_dfs.R
-# calls my function: dm_om_wf_lf_data()
-#########################################################
-  #geneL_normal  = c("pnca")
-  #geneL_na_dy   = c("gid")
-  geneL_na      = c("gid", "rpob")
-  geneL_dy      = c("gid")
-  geneL_ppi2    = c("alr", "embb", "katg", "rpob")
-  
-all_dm_om_df = dm_om_wf_lf_data(df = merged_df3, gene_name = gene)
-
-wf_duet      = all_dm_om_df[['wf_duet']]
-lf_duet      = all_dm_om_df[['lf_duet']]
-
-wf_mcsm_lig  = all_dm_om_df[['wf_mcsm_lig']]
-lf_mcsm_lig  = all_dm_om_df[['lf_mcsm_lig']]
-
-wf_foldx     = all_dm_om_df[['wf_foldx']]
-lf_foldx     = all_dm_om_df[['lf_foldx']]
-
-wf_deepddg   = all_dm_om_df[['wf_deepddg']]
-lf_deepddg   = all_dm_om_df[['lf_deepddg']]
-
-wf_dynamut2  = all_dm_om_df[['wf_dynamut2']]
-lf_dynamut2  = all_dm_om_df[['lf_dynamut2']]
-
-wf_consurf   = all_dm_om_df[['wf_consurf']]
-lf_consurf   = all_dm_om_df[['lf_consurf']]
-
-wf_snap2     = all_dm_om_df[['wf_snap2']]
-lf_snap2     = all_dm_om_df[['lf_snap2']]
-
-if (tolower(gene)%in%geneL_na){
-wf_mcsm_na   = all_dm_om_df[['wf_mcsm_na']]
-lf_mcsm_na   = all_dm_om_df[['lf_mcsm_na']]
-}
-
-if (tolower(gene)%in%geneL_ppi2){
-wf_mcsm_ppi2 = all_dm_om_df[['wf_mcsm_ppi2']]
-lf_mcsm_ppi2 = all_dm_om_df[['lf_mcsm_ppi2']]
-}
-
-if (tolower(gene)%in%geneL_dy){
-wf_dynamut   = all_dm_om_df[['wf_dynamut']]
-lf_dynamut   = all_dm_om_df[['lf_dynamut']]
-
-wf_encomddg  = all_dm_om_df[['wf_encomddg']]
-lf_encomddg  = all_dm_om_df[['lf_encomddg']]
-
-wf_encomdds  = all_dm_om_df[['wf_encomdds']]
-lf_encomdds  = all_dm_om_df[['lf_encomdds']]
-
-wf_sdm       = all_dm_om_df[['wf_sdm']]
-lf_sdm       = all_dm_om_df[['lf_sdm']]
-
-wf_mcsm      = all_dm_om_df[['wf_mcsm']]
-lf_mcsm      = all_dm_om_df[['lf_mcsm']]
-}

scripts/plotting/get_plotting_dfs.R

@@ -112,7 +112,44 @@ cat(s1)
 #source("other_plots_data.R")
 ####################################################################
 
-#source(paste0(plot_script_path, "dm_om_data.R"))
+#source(paste0(plot_script_path, "dm_om_data.R")) # calling the function directly instead
+geneL_normal  = c("pnca")
+geneL_na      = c("gid", "rpob")
+geneL_ppi2    = c("alr", "embb", "katg", "rpob")
+
+all_dm_om_df = dm_om_wf_lf_data(df = merged_df3, gene_name = gene)
+
+wf_duet      = all_dm_om_df[['wf_duet']]
+lf_duet      = all_dm_om_df[['lf_duet']]
+
+wf_mcsm_lig  = all_dm_om_df[['wf_mcsm_lig']]
+lf_mcsm_lig  = all_dm_om_df[['lf_mcsm_lig']]
+
+wf_foldx     = all_dm_om_df[['wf_foldx']]
+lf_foldx     = all_dm_om_df[['lf_foldx']]
+
+wf_deepddg   = all_dm_om_df[['wf_deepddg']]
+lf_deepddg   = all_dm_om_df[['lf_deepddg']]
+
+wf_dynamut2  = all_dm_om_df[['wf_dynamut2']]
+lf_dynamut2  = all_dm_om_df[['lf_dynamut2']]
+
+wf_consurf   = all_dm_om_df[['wf_consurf']]
+lf_consurf   = all_dm_om_df[['lf_consurf']]
+
+wf_snap2     = all_dm_om_df[['wf_snap2']]
+lf_snap2     = all_dm_om_df[['lf_snap2']]
+
+if (tolower(gene)%in%geneL_na){
+  wf_mcsm_na   = all_dm_om_df[['wf_mcsm_na']]
+  lf_mcsm_na   = all_dm_om_df[['lf_mcsm_na']]
+}
+
+if (tolower(gene)%in%geneL_ppi2){
+  wf_mcsm_ppi2 = all_dm_om_df[['wf_mcsm_ppi2']]
+  lf_mcsm_ppi2 = all_dm_om_df[['lf_mcsm_ppi2']]
+}
+
 s2 = c("\nSuccessfully sourced other_plots_data.R")
 cat(s2)
 

scripts/plotting/running_plotting_scripts.txt

@@ -136,6 +136,16 @@ note:
  - fa flag has default if not supplied 
  - fb flag has default if not supplied
  
+ 
+#====================================
+#dm_om plots
+#==================================== 
+dm_om_data.R --> one version in script that was being sourced by get_plotting_dfs.R
+dm_om_data.R --> another one is a function in function
+
+dm_om_data.R the script vesion has been moved to redundant and the content directly put in
+ge_plotting_dfs.R
+ 
 ########################################################################
 # TODO
 Delete: dirs.R