From 164113f66541cf274aadb183fa1f7343245a6ff5 Mon Sep 17 00:00:00 2001 From: Tanushree Tunstall Date: Fri, 5 Aug 2022 14:44:36 +0100 Subject: [PATCH] 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 | 62 ------------------- scripts/plotting/get_plotting_dfs.R | 39 +++++++++++- scripts/plotting/running_plotting_scripts.txt | 10 +++ 3 files changed, 48 insertions(+), 63 deletions(-) delete mode 100644 scripts/plotting/dm_om_data.R diff --git a/scripts/plotting/dm_om_data.R b/scripts/plotting/dm_om_data.R deleted file mode 100644 index 97e5e7a..0000000 --- a/scripts/plotting/dm_om_data.R +++ /dev/null @@ -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']] -} diff --git a/scripts/plotting/get_plotting_dfs.R b/scripts/plotting/get_plotting_dfs.R index e1423d0..0810d62 100644 --- a/scripts/plotting/get_plotting_dfs.R +++ b/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) diff --git a/scripts/plotting/running_plotting_scripts.txt b/scripts/plotting/running_plotting_scripts.txt index 369bc4b..9021fa0 100644 --- a/scripts/plotting/running_plotting_scripts.txt +++ b/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