various changes
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1 changed files with 57 additions and 43 deletions
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@ -17,6 +17,7 @@ wideP_consurf2 <- function(plot_df
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, aa_pos_lig1 = NULL
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, aa_pos_lig2 = NULL
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, aa_pos_lig3 = NULL
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, active_aa_pos = NULL
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, xvar_colname = "position"
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, yvar_colname = "consurf_score"
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@ -70,10 +71,9 @@ wideP_consurf2 <- function(plot_df
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, tH0 = 0.3
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# Custom 3: x-axis: geom tiles ~ active sites and ligand
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, annotate_active_sites = F
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, annotate_active_sites = T
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, drug_aa_colour = "purple"
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, active_aa_pos = NULL
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, active_aa_colour = "brown"
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, aa_colour_lig1 = "blue"
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@ -86,6 +86,7 @@ wideP_consurf2 <- function(plot_df
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, tpos3 = 0
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, default_gt_clr = "white"
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, build_plot_df=FALSE
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, debug=FALSE
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){
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@ -181,47 +182,60 @@ wideP_consurf2 <- function(plot_df
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# Build Data with colours
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# ~ on active sites
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#==========================
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aa_colour_colname = "bg_all"
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aa_colour_colname1 = "col_bg1"
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aa_colour_colname2 = "col_bg2"
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aa_colour_colname3 = "col_bg3"
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if(annotate_active_sites) {
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cat("\nAnnotation for xvar requested. Building colours for annotation...")
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aa_colour_colname = "bg_all"
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aa_colour_colname1 = "col_bg1"
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aa_colour_colname2 = "col_bg2"
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aa_colour_colname3 = "col_bg3"
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#--------------------------------------------------
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# column colour 0: Active site + drug binding sites
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#--------------------------------------------------
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plot_df[[aa_colour_colname]] = ifelse(plot_df[[xvar_colname]]%in%aa_pos_drug
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, drug_aa_colour
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, ifelse(plot_df[[xvar_colname]]%in%active_aa_pos
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, active_aa_colour, default_gt_clr ))
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plot_df[[aa_colour_colname]]
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cat("\nColumn created 'bg_all':", length(plot_df[[aa_colour_colname]]))
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#------------------------------------------------
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# column colour 1: Ligand 1 + drug binding sites
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#------------------------------------------------
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cat("\nAssigning colours to drug binding and ligand-1 binding residues")
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plot_df[[aa_colour_colname1]] = plot_df[[aa_colour_colname]]
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plot_df[[aa_colour_colname1]] = ifelse(plot_df[[xvar_colname]]%in%aa_pos_lig1
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, aa_colour_lig1, plot_df[[aa_colour_colname]])
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#------------------------------------------------
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# column colour 2: Ligand 2
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#------------------------------------------------
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plot_df[[aa_colour_colname2]] = plot_df[[aa_colour_colname1]]
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plot_df[[aa_colour_colname2]] = ifelse(plot_df[[xvar_colname]]%in%aa_pos_lig2
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, aa_colour_lig2, plot_df[[aa_colour_colname1]])
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#------------------------------------------------
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# column colour 3: Ligand 3
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#------------------------------------------------
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plot_df[[aa_colour_colname3]] = plot_df[[aa_colour_colname2]]
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plot_df[[aa_colour_colname3]] = ifelse(plot_df[[xvar_colname]]%in%aa_pos_lig3
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, aa_colour_lig3, plot_df[[aa_colour_colname2]])
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}
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if (build_plot_df) {
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if(annotate_active_sites) {
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cat("\nAnnotation for xvar requested. Building colours for annotation...")
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#--------------------------------------------------
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# column colour 0: Active site + drug binding sites
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#--------------------------------------------------
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plot_df[[aa_colour_colname]] = ifelse(plot_df[[xvar_colname]]%in%aa_pos_drug
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, drug_aa_colour
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, ifelse(plot_df[[xvar_colname]]%in%active_aa_pos
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, active_aa_colour, default_gt_clr ))
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plot_df[[aa_colour_colname]]
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cat("\nColumn created 'bg_all':", length(plot_df[[aa_colour_colname]]))
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#------------------------------------------------
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# column colour 1: Ligand 1 + drug binding sites
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#------------------------------------------------
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cat("\nAssigning colours to drug binding and ligand-1 binding residues")
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plot_df[[aa_colour_colname1]] = plot_df[[aa_colour_colname]]
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plot_df[[aa_colour_colname1]] = ifelse(plot_df[[xvar_colname]]%in%aa_pos_lig1
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, aa_colour_lig1, plot_df[[aa_colour_colname]])
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#------------------------------------------------
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# column colour 2: Ligand 2
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#------------------------------------------------
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plot_df[[aa_colour_colname2]] = plot_df[[aa_colour_colname1]]
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plot_df[[aa_colour_colname2]] = ifelse(plot_df[[xvar_colname]]%in%aa_pos_lig2
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, aa_colour_lig2, plot_df[[aa_colour_colname1]])
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#------------------------------------------------
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# column colour 3: Ligand 3
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#------------------------------------------------
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plot_df[[aa_colour_colname3]] = plot_df[[aa_colour_colname2]]
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plot_df[[aa_colour_colname3]] = ifelse(plot_df[[xvar_colname]]%in%aa_pos_lig3
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, aa_colour_lig3, plot_df[[aa_colour_colname2]])
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}
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} else {
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# set these to the string "DUMMY" so that the build-up-the-tiles bit works
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aa_pos_drug = "DUMMY"
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aa_pos_lig1 = "DUMMY"
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active_aa_pos = "DUMMY"
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if (aa_colour_colname2 %in% colnames(merged_df3)) {
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aa_pos_lig2 = "DUMMY"
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if (aa_colour_colname3 %in% colnames(merged_df3)) {
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aa_pos_lig2 = "DUMMY"
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}
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}
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}
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###################
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# start plot
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###################
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@ -456,7 +470,7 @@ wideP_consurf2 <- function(plot_df
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cat("\nDone Plot with 1 ligand")
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} else {cat("\n3 Lig Plot condition FAIL")}
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} else {cat("\n1 Lig Plot condition FAIL")}
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#-----------------------------------
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# Add2plot:NO ligands
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