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generated lineage barplots and corr plots for conservation

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This commit is contained in:
Tanushree Tunstall 2022-08-04 19:48:09 +01:00
parent 424c1d184d
commit 14f8f5d6d4
3 changed files with 52 additions and 9 deletions
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40
scripts/plotting/plotting_thesis/corr_plots_thesis.R
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@ -137,6 +137,46 @@ my_corr_pairs(corr_data_all = corr_df_ppi2
, corr_value_size = 1)
dev.off()
# FIXME: ADD distance
#==================
# mCSSM-NA affinity
#==================
# FIXME: ADD PROVEAN
####################################################
# CONSERVATION
####################################################
corr_df_cons = corr_plotdf[, corr_conservation_cols]
color_coln = which(colnames(corr_df_cons) == "dst_mode")
end = which(colnames(corr_df_cons) == drug)
ncol_omit = 2
corr_end = end-ncol_omit
#---------------------------
# Output: Conservation corrP
#----------------------------
corr_consP = paste0(outdir_images
,tolower(gene)
,"_corr_ppi2.svg" )
cat("Corr plot conservation coloured dots:", corr_consP)
svg(corr_consP, width = 10, height = 10)
my_corr_pairs(corr_data_all = corr_df_cons
, corr_cols = colnames(corr_df_cons[1:corr_end])
, corr_method = "spearman" # other options: "pearson" or "kendall"
, colour_categ_col = colnames(corr_df_cons[color_coln]) #"dst_mode"
, categ_colour = c("red", "blue")
, density_show = F
, hist_col = "coral4"
, dot_size = 2
, ats = 1.5
, corr_lab_size = 3
, corr_value_size = 1)
dev.off()

4
scripts/plotting/plotting_thesis/lineage_barplots_combined.R
View file

@ -1,5 +1,6 @@
# get plotting_dfs()
# using dfs [lf and wf] from lineage_dfL
# FIXME: add SNP diversity as the title
#===============================
# lineage sample and SNP count
#===============================
@ -54,7 +55,7 @@ lin_diversityP = lin_count_bp_diversity(lf_data = lineage_dfL[['lin_wf']]
#=============================================
lineage_bp_CL = paste0(outdir_images
,tolower(gene)
,"_lineage_bp_CL.svg")
,"_lineage_bp_CL_Tall.svg")
cat("Lineage barplots:", lineage_bp_CL)
svg(lineage_bp_CL, width = 8, height = 15)
@ -62,6 +63,7 @@ svg(lineage_bp_CL, width = 8, height = 15)
cowplot::plot_grid(lin_countP, lin_diversityP
#, labels = c("(a)", "(b)", "(c)", "(d)")
, nrow = 2
# , ncols = 2
, labels = "AUTO"
, label_size = 25)

7
scripts/plotting/plotting_thesis/preformatting.R
View file

@ -235,11 +235,12 @@ corr_ppi2_colnames = c("mCSM-PPI2"
, "dst_mode"
, drug)
corr_conservation = c("Consurf"
#FIXME: Add provean
corr_conservation_cols = c("Consurf"
, "SNAP2"
, "MAF"
, "Log (OR)"
, "-Log (P)"
, "interface_dist"
, "dst_mode"
, drug)