627 lines
24 KiB
R
627 lines
24 KiB
R
#!/usr/bin/env Rscript
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#########################################################
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# TASK: function for wide plot
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#with consurf score and error bars
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#position numbers coloured by
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# - ligand distance
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# - active site residues
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#########################################################
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#==========================================================
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# wideP():
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# input args
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#==========================================================
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wideP_consurf <- function(plotdf
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, xvar_colname = "position"
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, yvar_colname = "consurf_score"
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, yvar_colourN_colname = "consurf_colour_rev" # num from 0-1
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, plot_error_bars = T
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, upper_EB_colname = "consurf_ci_upper"
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, lower_EB_colname = "consurf_ci_lower"
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, plot_type = "point" # default is point
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, point_colours
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, p_size = 2
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, leg_title1 = ""
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, leg_labels = c("0": "Insufficient Data"
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, "1": "Variable"
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, "2", "3", "4", "5", "6", "7", "8"
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, "9": "Conserved")
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, panel_col = "black"
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, panel_col_fill = "black"
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# axes title and label sizes
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, x_axls = 12 # x-axis label size
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, y_axls = 15 # y-axis label size
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, x_axts = 12 # x-axis text size
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, y_axts = 12 # y-axis text size
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, default_xtc = "black" # x-axis text colour
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, ptitle = ""
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, xlab = ""
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, ylab = ""
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, pts = 20
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# plot margins
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, t_margin = 0.5
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, r_margin = 0.5
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, b_margin = 1
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, l_margin = 1
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, unit_margin = "cm"
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# Custom 1: x-axis: text colour
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, xtext_colour_aa = F
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, xtext_colour_aa1 = active_aa_pos
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, xtext_colour_aa2 = aa_pos_drug
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, xtext_colours = c("purple", "brown", "black")
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# Custom 2: x-axis: geom tiles ~ lig distance
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, A_xvar_lig = T
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, leg_title2 = "Ligand Distance"
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, lig_dist_colname = LigDist_colname # from globals
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, lig_dist_colours = c("green", "yellow", "orange", "red")
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, tpos0 = 0 # 0 is a magic number that does my sensible default
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, tW0 = 1
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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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, A_xvar_aa = F
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, aa_pos_drug = NULL
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, drug_aa_colour = "purple"
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, tW = 1
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, tH = 0.2
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, active_aa_pos = NULL
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, active_aa_colour = "brown"
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, aa_pos_lig1 = NULL
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, aa_colour_lig1 = "blue"
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, tpos1 = 0
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, aa_pos_lig2 = NULL
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, aa_colour_lig2 = "cyan"
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, tpos2 = 0
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, aa_pos_lig3 = NULL
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, aa_colour_lig3 = "cornflowerblue"
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, tpos3 = 0
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, default_gt_clr = "white"
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, debug=FALSE
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){
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if(missing(point_colours)){
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temp_cols = colorRampPalette(c("seagreen", "sienna3"))(30)
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point_colours = temp_cols
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}else{
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point_colours = point_colours
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}
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###############################
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# custom 1: x-axis text colour
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##############################
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if (xtext_colour_aa){
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positionF <- levels(as.factor(plotdf[[xvar_colname]]))
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length(positionF)
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aa_pos_colours = ifelse(positionF%in%xtext_colour_aa1, xtext_colours[1]
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, ifelse(positionF%in%xtext_colour_aa2
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, xtext_colours[2]
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, xtext_colours[3]))
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}else{
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aa_pos_colours = default_xtc
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}
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################################################
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# Custom 2: x-axis geom tiles ~ lig distance
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################################################
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#=========================
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# Build data with colours
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# ~ ligand distance
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#=========================
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if (A_xvar_lig){
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cat("\nAnnotating x-axis ~", lig_dist_colname, "requested...")
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#-------------------------------------
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# round column values: to colour by
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#--------------------------------------
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#plotdf = plotdf[order(plotdf[[lig_dist_colname]]),]
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plotdf['lig_distR'] = round(plotdf[[lig_dist_colname]], digits = 0)
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head(plotdf['lig_distR'])
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#-------------------------------------
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# ligand distance range, min, max, etc
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#--------------------------------------
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lig_min = min(round(plotdf[[lig_dist_colname]]), na.rm = T); lig_min
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lig_max = max(round(plotdf[[lig_dist_colname]]), na.rm = T); lig_max
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lig_mean = round(mean(round(plotdf[[lig_dist_colname]]), na.rm = T)); lig_mean
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#-------------------------------------
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# Create mapping colour key
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#--------------------------------------
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# sorting removes NA, so that n_colours == length(ligD_valsR)
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n_colours = length(sort(unique(round(plotdf[[lig_dist_colname]], digits = 0)))); n_colours
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lig_cols = colorRampPalette(lig_dist_colours)(n_colours); lig_cols
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ligD_valsR = sort(unique(round(plotdf[[lig_dist_colname]], digits = 0))); ligD_valsR
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length(ligD_valsR)
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if (n_colours == length(ligD_valsR)) {
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cat("\nStarting: mapping b/w"
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, lig_dist_colname
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, "and colours")
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}else{
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cat("\nCannot start mapping b/w", lig_dist_colname, "and colours..."
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, "\nLength mismatch:"
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, "No. of colours: ", n_colours
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, "\nValues to map:", length(ligD_valsR))
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}
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ligDcolKey <- data.frame(ligD_colours = lig_cols
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, lig_distR = ligD_valsR); ligDcolKey
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names(ligDcolKey)
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cat("\nSuccessful: Mapping b/w", lig_dist_colname, "and colours")
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#-------------------------------------
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# merge colour key with plotdf
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#--------------------------------------
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plotdf = merge(plotdf, ligDcolKey, by = 'lig_distR')
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plotdf_check = as.data.frame(cbind(position = plotdf[[xvar_colname]]
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, ligD = plotdf[[lig_dist_colname]]
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, ligDR = plotdf$lig_distR
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, ligD_cols = plotdf$ligD_colours))
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} else{
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plotdf = plotdf
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}
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###############################################
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# Custom 3: x-axis geom tiles ~ active sites
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################################################
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#==========================
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# Build Data with colours
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# ~ on active sites
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#==========================
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if(A_xvar_aa) {
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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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plotdf[[aa_colour_colname]] = ifelse(plotdf[[xvar_colname]]%in%aa_pos_drug
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, drug_aa_colour
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, ifelse(plotdf[[xvar_colname]]%in%active_aa_pos
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, active_aa_colour, default_gt_clr ))
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plotdf[[aa_colour_colname]]
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cat("\nColumn created 'bg_all':", length(plotdf[[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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plotdf[[aa_colour_colname1]] = plotdf[[aa_colour_colname]]
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plotdf[[aa_colour_colname1]] = ifelse(plotdf[[xvar_colname]]%in%aa_pos_lig1
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, aa_colour_lig1, plotdf[[aa_colour_colname]])
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# plotdf[[aa_colour_colname1]] = ifelse( plotdf[[xvar_colname]]%in%active_aa_pos
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# , drug_aa_colour
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# , ifelse(plotdf[[xvar_colname]]%in%aa_pos_lig1
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# , aa_colour_lig1, default_gt_clr))
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#------------------------------------------------
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# column colour 2: Ligand 2
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#------------------------------------------------
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plotdf[[aa_colour_colname2]] = plotdf[[aa_colour_colname1]]
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plotdf[[aa_colour_colname2]] = ifelse(plotdf[[xvar_colname]]%in%aa_pos_lig2
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, aa_colour_lig2, plotdf[[aa_colour_colname1]])
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#------------------------------------------------
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# column colour 3: Ligand 3
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#------------------------------------------------
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plotdf[[aa_colour_colname3]] = plotdf[[aa_colour_colname2]]
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plotdf[[aa_colour_colname3]] = ifelse(plotdf[[xvar_colname]]%in%aa_pos_lig3
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, aa_colour_lig3, plotdf[[aa_colour_colname2]])
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}
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###################
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# start plot
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###################
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#-------------------
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# x and y axis
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# range, scale, etc
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#-------------------
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my_xlim = length(unique(plotdf[[xvar_colname]])); my_xlim
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ymin = min(plotdf[[yvar_colname]]); ymin
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ymax = max(plotdf[[yvar_colname]]); ymax
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# DEBUG
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# x_factor = as.factor(plotdf[[xvar_colname]])
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# y_colour_factor = as.factor(plotdf[[yvar_colourN_colname]])
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# cat('XXXX THIS:', str(x_factor))
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#
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# g = ggplot(plotdf, aes_string(x = x_factor)
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# , y = yvar_colname
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# , colour = y_colour_factor)
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g = ggplot(plotdf, aes_string(x = sprintf("factor(%s)", xvar_colname)
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, y = yvar_colname
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, colour = sprintf("factor(%s)", yvar_colourN_colname)
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))
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# g = ggplot(plotdf, aes_string(x = "position")
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# , y = "consurf_score"
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# , colour = "consurf_colour_rev")
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# g = ggplot(plotdf, aes_string(x = "position")
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# , y = "consurf_score"
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# , colour = "consurf_colour_rev")
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# DEBUG
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#g0=g
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"if SPECIAL do SPECIAL THING, otherwise do NORMAL THING"
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if (plot_type == "bar"){
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g0 = g +
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geom_bar(stat = "identity")
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}
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else{
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g0 = g +
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coord_cartesian(xlim = c(1, my_xlim)
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, ylim = c(ymin, ymax)
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, clip = "off") +
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geom_point(size = p_size) +
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scale_colour_manual(values = point_colours)
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# , labels = leg_labels
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# , name = leg_title1)
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}
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if (plot_error_bars){
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g0 = g0 +
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geom_errorbar(aes(ymin = eval(parse(text = lower_EB_colname))
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, ymax = eval(parse(text = upper_EB_colname))
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))
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}else{
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g0 = g0
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}
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#---------------------
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# add axis formatting
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#---------------------
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g1 = g0 + theme( axis.text.x = element_text(size = x_axts
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, angle = 90
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, hjust = 1
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, vjust = 0.4
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, face = "bold"
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, colour = aa_pos_colours)
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, axis.text.y = element_text(size = y_axts
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, angle = 0
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, hjust = 1
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, vjust = 0)
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, axis.title.x = element_text(size = x_axls)
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, axis.title.y = element_text(size = y_axls )
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, panel.background = element_rect(fill = panel_col_fill, color = panel_col)
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, panel.grid.major = element_line(color = "black")
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, panel.grid.minor = element_line(color = "black")
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, plot.title = element_text(size = pts
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, hjust = 0.5)
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, plot.margin = margin(t = t_margin
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, r = r_margin
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, b = b_margin
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, l = l_margin
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, unit = unit_margin))+
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guides(colour = guide_legend(title = "ConsurfXXXX")) +
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labs(title = ptitle
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, x = xlab
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, y = ylab)
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#------------------
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#Extract legend1
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#------------------
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# yayy
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g1_leg = ggplot(plotdf, aes_string(x = sprintf("factor(%s)"
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, xvar_colname) ))
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g1_leg = g1_leg + geom_bar(); g1_leg
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g1_leg = g1_leg + geom_bar(aes_string(fill = sprintf("factor(%s)"
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, yvar_colourN_colname)))
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g1_leg = g1_leg + scale_fill_manual(values = consurf_palette2 , name = leg_title1)
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g1_leg
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legend1 = get_legend(g1_leg)
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#####################################################
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#============================================
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# x-axis: geom_tiles ~ ligand distance
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#============================================
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#-------
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# plot
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#-------
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if(A_xvar_lig){ # 0 is a magic number that does my sensible default
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if (tpos0 == 0){
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tpos0 = ymin-0.5
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}
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if (tpos1 == 0){
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tpos1 = ymin-0.65
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}
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if (tpos2 == 0){
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tpos2 = ymin-0.75
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}
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if (tpos3 == 0){
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tpos3 = ymin-0.85
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}
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cat("\nColouring x-axis aa based on", lig_dist_colname
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, "\nNo. of colours:", n_colours)
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g2 = g1 + geom_tile(aes(, tpos0
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, width = tW0
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, height = tH0)
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, fill = plotdf$ligD_colours
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, colour = plotdf$ligD_colours
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, linetype = "blank")
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#cat("Nrows of plot df", length(plotdf$ligD_colours))
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out = g2
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#
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# #------------------
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# # Extract legend2
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# #------------------
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# labels = seq(lig_min, lig_max, len = 5); labels
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# labelsD = round(labels, digits = 0); labelsD
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#
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# g2_leg = g1 +
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# geom_tile(aes(fill = .data[[lig_dist_colname]])
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# , colour = "white") +
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# scale_fill_gradient2(midpoint = lig_mean
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# , low = "green"
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# , mid = "yellow"
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# , high = "red"
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# , breaks = labels
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# #, n.breaks = 11
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# #, minor_breaks = c(2, 4, 6, 8, 10)
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# , limits = c(lig_min, lig_max)
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# , labels = labelsD
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# , name = leg_title2)
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#
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# legend2 = get_legend(g2_leg)
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#
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# }else{
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# out = g1
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# }
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######################################################
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#------------------
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# Extract legend2
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#------------------
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labels = seq(lig_min, lig_max, len = 5); labels
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labelsD = round(labels, digits = 0); labelsD
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g2_leg = ggplot(plotdf, aes_string(x = sprintf("factor(%s)", xvar_colname)
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, y = yvar_colname)
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) +
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geom_tile(aes(fill = .data[[lig_dist_colname]])
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, colour = "white") +
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scale_fill_gradient2(midpoint = lig_mean
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, low = "green"
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, mid = "yellow"
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, high = "red"
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, breaks = labels
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#, n.breaks = 11
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#, minor_breaks = c(2, 4, 6, 8, 10)
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, limits = c(lig_min, lig_max)
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, labels = labelsD
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, name = leg_title2)
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legend2 = get_legend(g2_leg)
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}else{
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out = g1
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}
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#####################################################
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# #============================================
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# # x-axis: geom_tiles ~ ligand distance
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# #============================================
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# if(A_xvar_lig){
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# cat("\nColouring x-axis aa based on", lig_dist_colname
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# , "\nNo. of colours:", n_colours)
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#
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# g2 = g1 + geom_tile(aes(, tpos0
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# , width = tW0
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# , height = tH0)
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# , fill = plotdf$ligD_colours
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# , colour = plotdf$ligD_colours
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# , linetype = "blank")
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#
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# #cat("Nrows of plot df", length(plotdf$ligD_colours))
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# out = g2
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# }else{
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# out = g1
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# }
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#
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############################################################################################
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#==============================================
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# x-axis: geom_tiles ~ active sites and others
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#==============================================
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if(A_xvar_aa){
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#tpos = 0
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#tW = 1
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#tH = 0.2
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#---------------------
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# Add2plot: 3 ligands
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#---------------------
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if (all(!is.null(active_aa_pos) &&
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!is.null(aa_pos_drug) &&
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!is.null(aa_pos_lig1) && !is.null(aa_pos_lig2) && !is.null(aa_pos_lig3))) {
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if (debug){
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cat("\n\nAnnotating xvar with active, drug binding, and Lig 1&2&3 sites")
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cat("\nCreating column colours, column name:", aa_colour_colname3)
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cat("\nDoing Plot with 3 ligands")
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}
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out = out + geom_tile(aes(,tpos3
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, width = tW
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, height = tH )
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, fill = plotdf[[aa_colour_colname3]]
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, colour = plotdf[[aa_colour_colname3]]
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, linetype = "solid") +
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geom_tile(aes(, tpos2
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, width = tW
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, height = tH )
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, fill = plotdf[[aa_colour_colname2]]
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, colour = plotdf[[aa_colour_colname2]]
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, linetype = "solid")+
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geom_tile(aes(, tpos1
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, width = tW
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, height = tH)
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, fill = plotdf[[aa_colour_colname1]]
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, colour = plotdf[[aa_colour_colname1]]
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, linetype = "solid")
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if (debug){
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cat("\nDone Plot with 3 ligands")
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}
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}
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#---------------------
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# Add2plot: 2 ligands
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#---------------------
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if (all(!is.null(active_aa_pos) &&
|
|
!is.null(aa_pos_drug) &&
|
|
!is.null(aa_pos_lig1) && !is.null(aa_pos_lig2) && is.null(aa_pos_lig3))) {
|
|
if (debug){
|
|
cat("\n\nAnnotating xvar with active, drug binding, and Lig 1&2 sites")
|
|
cat("\nCreating column colours, column name:", aa_colour_colname2)
|
|
|
|
cat("\nDoing Plot with 2 ligands")
|
|
}
|
|
out = out +
|
|
geom_tile(aes(, tpos2
|
|
, width = tW
|
|
, height = tH)
|
|
, fill = plotdf[[aa_colour_colname2]]
|
|
, colour = plotdf[[aa_colour_colname2]]
|
|
, linetype = "solid")+
|
|
geom_tile(aes(, tpos1
|
|
, width = tW
|
|
, height = tH)
|
|
, fill = plotdf[[aa_colour_colname1]]
|
|
, colour = plotdf[[aa_colour_colname1]]
|
|
, linetype = "solid")
|
|
if (debug){
|
|
cat("\nDone Plot with 2 ligands")
|
|
}
|
|
}
|
|
|
|
#---------------------
|
|
# Add2plot: 1 ligand
|
|
#---------------------
|
|
if (all(!is.null(active_aa_pos) &&
|
|
!is.null(aa_pos_drug) &&
|
|
!is.null(aa_pos_lig1) && is.null(aa_pos_lig2) && is.null(aa_pos_lig3))) {
|
|
if (debug){
|
|
cat("\n\nAnnotating xvar with active, drug binding, and Lig 1 sites")
|
|
cat("\nCreating column colours, column name:", aa_colour_colname1)
|
|
|
|
cat("\nDoing Plot with 1 ligands")
|
|
}
|
|
out = out +
|
|
geom_tile(aes(, tpos1
|
|
, width = tW
|
|
, height = tH)
|
|
, fill = plotdf[[aa_colour_colname1]]
|
|
, colour = plotdf[[aa_colour_colname1]]
|
|
, linetype = "solid")
|
|
|
|
cat("\nDone Plot with 1 ligand")
|
|
|
|
}
|
|
|
|
#-----------------------------------
|
|
# Add2plot:NO ligands
|
|
# No Ligs: Just drug and active site
|
|
# DEFAULT: A_xvar_aa == TRUE
|
|
#----------------------------------
|
|
if (all(!is.null(active_aa_pos) &&
|
|
!is.null(aa_pos_drug) &&
|
|
is.null(aa_pos_lig1) &&
|
|
is.null(aa_pos_lig2) &&
|
|
is.null(aa_pos_lig3))) {
|
|
if (debug){
|
|
cat("\n\nAnnotating xvar with active and drug binding sites")
|
|
cat("\nCreating column colours, column name:", aa_colour_colname)
|
|
cat("\nDoing Plot with 0 ligands: active and drug site only")
|
|
}
|
|
out = out + geom_tile(aes(, tpos3
|
|
, width = tW
|
|
, height = tH)
|
|
, fill = plotdf[[aa_colour_colname]]
|
|
, colour = plotdf[[aa_colour_colname]]
|
|
, linetype = "solid")
|
|
if (debug){
|
|
cat("\nDone Plot with: Active and Drug sites")
|
|
}
|
|
}
|
|
}else{
|
|
cat("\nNo annotation for additional ligands on xvar requested")
|
|
}
|
|
#==============================================
|
|
if (A_xvar_lig){
|
|
legs = cowplot::plot_grid(legend1
|
|
, legend2
|
|
, ncol = 1
|
|
, align = "hv"
|
|
, rel_heights = c(2/4,3/4))
|
|
|
|
out2 = cowplot::plot_grid( out + theme(legend.position = "none")
|
|
, legs
|
|
, ncol = 2
|
|
, align = "hv"
|
|
, rel_widths = c(9/10, 0.4/10)
|
|
)
|
|
}else{
|
|
out2 = cowplot::plot_grid( out + theme(legend.position = "none")
|
|
, legend1
|
|
, ncol = 2
|
|
, align = "hv"
|
|
, rel_widths = c(9/10, 0.5/10)
|
|
)
|
|
}
|
|
#==============================================
|
|
|
|
|
|
#==============================================
|
|
# if (A_xvar_lig){
|
|
# legs = grid.arrange(legend1
|
|
# , legend2
|
|
# , ncol = 1
|
|
# , heights = c(3/4,1))
|
|
#
|
|
# out2 = grid.arrange( out + theme(legend.position = "none")
|
|
# , legs
|
|
# , ncol = 2
|
|
# , widths = c(9/10, 0.5/10)
|
|
# )
|
|
# }else{
|
|
# out2 = grid.arrange( out + theme(legend.position = "none")
|
|
# , legend1
|
|
# , ncol = 2
|
|
# , widths = c(9/10, 0.5/10)
|
|
# )
|
|
# }
|
|
#==============================================
|
|
return(out2)
|
|
#return(out2)
|
|
|
|
}
|
|
|
|
#############################################################
|
|
# end of function
|
|
#############################################################
|