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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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22
scripts/plotting/plotting_thesis/version1/basic_barplots.R
View file

@ -11,7 +11,7 @@
# , lts = 20 # legend text size
# , ltis = 22 # label title size
# , geom_ls = 10 # geom_label size
# , yaxis_title = "Number of nsSNPs"
# , yaxis_title = "Number of SAVs"
# , bp_plot_title = ""
# , label_categories = c("Destabilising", "Stabilising")
# , title_colour = "chocolate4"
@ -94,7 +94,7 @@ 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-lig"
, bar_fill_values = c("#F8766D", "#00BFC4")
@ -141,7 +141,7 @@ 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-ppi2"
, bar_fill_values = c("#F8766D", "#00BFC4")
@ -167,7 +167,7 @@ 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-NA"
, bar_fill_values = c("#F8766D", "#00BFC4")
@ -191,7 +191,7 @@ 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 = ""
@ -210,7 +210,7 @@ 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 = ""
@ -230,7 +230,7 @@ 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 = ""
@ -248,7 +248,7 @@ 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"
@ -263,7 +263,7 @@ 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 # from globals
@ -286,7 +286,7 @@ 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")
@ -359,7 +359,7 @@ 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

20
scripts/plotting/plotting_thesis/version1/basic_barplots_UPDATED.R
View file

@ -60,7 +60,7 @@ 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-lig"
, bar_fill_values = c("#F8766D", "#00BFC4")
@ -107,7 +107,7 @@ 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-ppi2"
, bar_fill_values = c("#F8766D", "#00BFC4")
@ -133,7 +133,7 @@ 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-NA"
, bar_fill_values = c("#F8766D", "#00BFC4")
@ -157,7 +157,7 @@ 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 = ""
@ -176,7 +176,7 @@ 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 = ""
@ -196,7 +196,7 @@ 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 = ""
@ -214,7 +214,7 @@ 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"
@ -229,7 +229,7 @@ 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 # from globals
@ -252,7 +252,7 @@ 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")
@ -325,7 +325,7 @@ 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

2
scripts/plotting/plotting_thesis/version1/preformatting.R
View file

@ -85,7 +85,7 @@ foo2 = foo[foo$ligand_distance<10,]
table(foo2$ligand_outcome)
#############################
# wide plots SNP
# wide plots SAV
# DRUG
length(aa_pos_drug); aa_pos_drug
drug = foo[foo$position%in%aa_pos_drug,]