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SNP -> SAV for thesis plots

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This commit is contained in:
Tanushree Tunstall 2023-02-19 17:43:22 +00:00
parent 777d3765cf
commit db7e2912e1
31 changed files with 145 additions and 145 deletions
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20
scripts/plotting/plotting_thesis/alr/basic_barplots_alr.R
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@ -65,7 +65,7 @@ mLigP = stability_count_bp(plotdf = df3_lig
, df_colname = "ligand_outcome"
#, leg_title = "mCSM-lig"
#, bp_plot_title = paste(common_bp_title, "ligand")
, yaxis_title = "Number of nsSNPs"
, yaxis_title = "Number of SAVs"
, leg_position = "none"
, subtitle_text = "mCSM\nLig"
, bar_fill_values = c("#F8766D", "#00BFC4")
@ -113,7 +113,7 @@ if (tolower(gene)%in%geneL_ppi2){
#, label_categories = labels_ppi2
#, bp_plot_title = paste(common_bp_title, "PP-interface")
, yaxis_title = "Number of nsSNPs"
, yaxis_title = "Number of SAVs"
, leg_position = "none"
, subtitle_text = "mCSM\nPPI2"
, bar_fill_values = c("#F8766D", "#00BFC4")
@ -138,7 +138,7 @@ if (tolower(gene)%in%geneL_na){
#, label_categories =
#, bp_plot_title = paste(common_bp_title, "Dist to NA")
, yaxis_title = "Number of nsSNPs"
, yaxis_title = "Number of SAVs"
, leg_position = "none"
, subtitle_text = "mCSM\nNA"
, bar_fill_values = c("#F8766D", "#00BFC4")
@ -162,7 +162,7 @@ common_bp_title = paste0("Sites <", DistCutOff, angstroms_symbol)
posC_lig = site_snp_count_bp(plotdf = df3_lig
, df_colname = "position"
, xaxis_title = "Number of nsSNPs"
, xaxis_title = "Number of SAVs"
, yaxis_title = "Number of Sites"
, subtitle_colour = "chocolate4"
, subtitle_text = ""
@ -180,7 +180,7 @@ posC_lig
if (tolower(gene)%in%geneL_ppi2){
posC_ppi2 = site_snp_count_bp(plotdf = df3_ppi2
, df_colname = "position"
, xaxis_title = "Number of nsSNPs"
, xaxis_title = "Number of SAVs"
, yaxis_title = "Number of Sites"
, subtitle_colour = "chocolate4"
, subtitle_text = ""
@ -199,7 +199,7 @@ if (tolower(gene)%in%geneL_ppi2){
if (tolower(gene)%in%geneL_na){
posC_nca = site_snp_count_bp(plotdf = df3_na
, df_colname = "position"
, xaxis_title = "Number of nsSNPs"
, xaxis_title = "Number of SAVs"
, yaxis_title = "Number of Sites"
, subtitle_colour = "chocolate4"
, subtitle_text = ""
@ -217,7 +217,7 @@ if (tolower(gene)%in%geneL_na){
#------------------------------
posC_all = site_snp_count_bp(plotdf = df3
, df_colname = "position"
, xaxis_title = "Number of nsSNPs"
, xaxis_title = "Number of SAVs"
, yaxis_title = "Number of Sites"
, subtitle_colour = "chocolate4"
, subtitle_text = "All mutations sites"
@ -233,7 +233,7 @@ consurfP = stability_count_bp(plotdf = df3
, df_colname = "consurf_outcome"
#, leg_title = "ConSurf"
#, label_categories = labels_consurf
, yaxis_title = "Number of nsSNPs"
, yaxis_title = "Number of SAVs"
, leg_position = "top"
, subtitle_text = "ConSurf"
, bar_fill_values = consurf_colours_no_isd # from globals
@ -262,7 +262,7 @@ duetP = stability_count_bp(plotdf = df3
, df_colname = "duet_outcome"
, leg_title = "mCSM-DUET"
#, label_categories = labels_duet
, yaxis_title = "Number of nsSNPs"
, yaxis_title = "Number of SAVs"
, leg_position = "none"
, subtitle_text = "mCSM-DUET"
, bar_fill_values = c("#F8766D", "#00BFC4")
@ -331,7 +331,7 @@ proveanP = stability_count_bp(plotdf = df3
, df_colname = "provean_outcome"
#, leg_title = "PROVEAN"
#, label_categories = labels_provean
, yaxis_title = "Number of nsSNPs"
, yaxis_title = "Number of SAVs"
, leg_position = "none" # top
, subtitle_text = "PROVEAN"
, bar_fill_values = c("#D01C8B", "#F1B6DA") # light pink and deep