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

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This commit is contained in:
Tanushree Tunstall 2022-08-05 14:44:36 +01:00
parent cc27ffe82f
commit 164113f665
3 changed files with 48 additions and 63 deletions
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62
scripts/plotting/dm_om_data.R
View file

@ -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']]
}

39
scripts/plotting/get_plotting_dfs.R
View file

@ -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)

10
scripts/plotting/running_plotting_scripts.txt
View file

@ -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