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added corr plot TODO for lineage counts

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This commit is contained in:
Tanushree Tunstall 2022-08-06 13:30:41 +01:00
parent 0e777108a9
commit f194b5ea4f
2 changed files with 30 additions and 7 deletions
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9
scripts/functions/corr_plot_data.R
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@ -18,9 +18,12 @@
# RETURNS: DF
# containing all the columns required for generating downstream correlation plots
# TO DO: SHINY
#1) Corr type?
#2)
# TODO: ADD
#lineage_count_all
#lineage_count_unique
#my_df['lineage_proportion'] = my_df['lineage_count_unique']/my_df['lineage_count_all']
#my_df['dist_lineage_proportion'] = my_df['lineage_count_unique']/total_mtblineage_uc
##################################################################
# LigDist_colname #from globals: plotting_globals.R
# ppi2Dist_colname #from globals: plotting_globals.R

28
scripts/plotting/plotting_thesis/corr_plots_thesis.R
View file

@ -1,10 +1,30 @@
#!/usr/bin/env Rscript
#source("~/git/LSHTM_analysis/config/alr.R")
source("~/git/LSHTM_analysis/config/embb.R")
#source("~/git/LSHTM_analysis/config/katg.R")
#source("~/git/LSHTM_analysis/config/gid.R")
#source("~/git/LSHTM_analysis/config/pnca.R")
#source("~/git/LSHTM_analysis/config/rpob.R")
# get plottting dfs
source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
####################################################
#=======
# output
#=======
outdir_images = paste0("~/git/Writing/thesis/images/results/", tolower(gene), "/")
#=======
# Input
#=======
merged_df3 = as.data.frame(merged_df3)
corr_plotdf = corr_data_extract(merged_df3
, gene = gene
, drug = drug
, extract_scaled_cols = F)
colnames(corr_plotdf)
colnames(corr_df_m3_f)
corr_plotdf = corr_df_m3_f # for downstream code
#================
# stability
#================
@ -179,7 +199,7 @@ corr_end = end-ncol_omit
#----------------------------
corr_consP = paste0(outdir_images
,tolower(gene)
,"_corr_ppi2.svg" )
,"_corr_conservation.svg" )
cat("Corr plot conservation coloured dots:", corr_consP)
svg(corr_consP, width = 10, height = 10)
@ -191,9 +211,9 @@ my_corr_pairs(corr_data_all = corr_df_cons
, categ_colour = c("red", "blue")
, density_show = F
, hist_col = "coral4"
, dot_size = 2
, dot_size =1.1
, ats = 1.5
, corr_lab_size = 3
, corr_lab_size = 2.5
, corr_value_size = 1)
dev.off()