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renamed count_vars_ML previous version as such

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This commit is contained in:
Tanushree Tunstall 2022-08-31 22:02:16 +01:00
parent 14e655eeeb
commit a5d22540e1
9 changed files with 336 additions and 185 deletions
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7
scripts/plotting/plotting_thesis/alr/gg_pairs_all_alr.R
View file

@ -1,12 +1,13 @@
source("~/git/LSHTM_analysis/config/alr.R")
source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
source("~/git/LSHTM_analysis/scripts/plotting/plotting_colnames.R")
#=======
# output
#=======
outdir_images = paste0("~/git/Writing/thesis/images/results/", tolower(gene), "/")
#outdir_images = paste0("/home/pub/Work/LSHTM/Thesis_Plots/pairs/")
#cat("plots will output to:", outdir_images)
cat("plots will output to:", outdir_images)
custom_cor <- function(
data,
@ -190,7 +191,7 @@ unmasked_vals
# Stability
#================
corr_ps_colnames = c(static_cols
, "DUET"
, "mCSM-DUET"
, "FoldX"
, "DeepDDG"
, "Dynamut2"

4
scripts/plotting/plotting_thesis/embb/basic_barplots_embb.R
View file

@ -7,8 +7,8 @@
#=============
# Data: Input
#==============
#source("~/git/LSHTM_analysis/config/embb.R")
#source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
source("~/git/LSHTM_analysis/config/embb.R")
source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
#cat("\nSourced plotting cols as well:", length(plotting_cols))

5
scripts/plotting/plotting_thesis/embb/gg_pairs_all_embb.R
View file

@ -1,5 +1,4 @@
#source("~/git/LSHTM_analysis/config/embb.R")
#source("~/git/LSHTM_analysis/scripts/plotting/plotting_colnames.R")
#source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
my_gg_pairs=function(plot_df, plot_title
@ -53,7 +52,7 @@ corr_plotdf = corr_data_extract(merged_df3
aff_dist_cols = colnames(corr_plotdf)[grep("Dist", colnames(corr_plotdf))]
static_cols = c("Log10(MAF)"
, "Log10(OR)"
#, "Log10(OR)"
)
############################################################
#=============================================
@ -85,7 +84,7 @@ unmasked_vals
# Stability
#================
corr_ps_colnames = c(static_cols
, "DUET"
, "mCSM-DUET"
, "FoldX"
, "DeepDDG"
, "Dynamut2"

2
scripts/plotting/plotting_thesis/gid/gg_pairs_all_gid.R
View file

@ -95,7 +95,7 @@ unmasked_vals
# Stability
#================
corr_ps_colnames = c(static_cols
, "DUET"
, "mCSM-DUET"
, "FoldX"
, "DeepDDG"
, "Dynamut2"

15
scripts/plotting/plotting_thesis/katg/gg_pairs_all_katg.R
View file

@ -1,6 +1,13 @@
#source("~/git/LSHTM_analysis/config/katg.R")
#source("~/git/LSHTM_analysis/scripts/plotting/plotting_colnames.R")
#source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
source("~/git/LSHTM_analysis/config/katg.R")
source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
#=======
# output
#=======
outdir_images = paste0("~/git/Writing/thesis/images/results/", tolower(gene), "/")
cat("plots will output to:", outdir_images)
my_gg_pairs=function(plot_df, plot_title
, tt_args_size = 2.5
@ -85,7 +92,7 @@ unmasked_vals
# Stability
#================
corr_ps_colnames = c(static_cols
, "DUET"
, "mCSM-DUET"
, "FoldX"
, "DeepDDG"
, "Dynamut2"

8
scripts/plotting/plotting_thesis/katg/katg_ORandSNP_results.R
View file

@ -203,6 +203,14 @@ write.csv(bar_or, paste0(outdir_stats, "katg_OR_10.csv"))
top10_or$position[top10_or$position%in%active_aa_pos]
# maf
bar_maf = bar_or[order(bar_or$maf_percent
, bar_or$ligand_distance
# bar_or$nca_dist
, bar_or$interface_dist
, decreasing = T), ]
head(bar_maf)
#########################################################
# closest most sig
bar_or_lig = bar_or[bar_or$ligand_distance<10,]

6
scripts/plotting/plotting_thesis/rpob/basic_barplots_rpob.R
View file

@ -7,10 +7,10 @@
#=============
# Data: Input
#==============
#source("~/git/LSHTM_analysis/config/rpob.R")
#source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
source("~/git/LSHTM_analysis/config/rpob.R")
source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
#cat("\nSourced plotting cols as well:", length(plotting_cols))
cat("\nSourced plotting cols as well:", length(plotting_cols))
####################################################
class(merged_df3)