consurf plot: add debug option. logoP SNP: distance flame tiles
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2 changed files with 230 additions and 219 deletions
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@ -13,99 +13,100 @@
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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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){
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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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}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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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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@ -127,7 +128,7 @@ wideP_consurf <- function(plotdf
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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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@ -170,9 +171,9 @@ wideP_consurf <- function(plotdf
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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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} 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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@ -182,7 +183,7 @@ wideP_consurf <- function(plotdf
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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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@ -247,11 +248,11 @@ wideP_consurf <- function(plotdf
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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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, 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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@ -273,22 +274,22 @@ wideP_consurf <- function(plotdf
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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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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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, 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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@ -298,22 +299,22 @@ wideP_consurf <- function(plotdf
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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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, 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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@ -364,39 +365,39 @@ wideP_consurf <- function(plotdf
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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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, 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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# #------------------
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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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@ -404,7 +405,7 @@ wideP_consurf <- function(plotdf
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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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) +
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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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@ -423,7 +424,7 @@ wideP_consurf <- function(plotdf
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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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@ -445,7 +446,7 @@ wideP_consurf <- function(plotdf
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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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#==============================================
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# x-axis: geom_tiles ~ active sites and others
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#==============================================
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@ -454,48 +455,53 @@ wideP_consurf <- function(plotdf
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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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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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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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cat("\nDone Plot with 3 ligands")
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}
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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") +
|
||||
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 3 ligands")
|
||||
}
|
||||
}
|
||||
#---------------------
|
||||
# Add2plot: 2 ligands
|
||||
#---------------------
|
||||
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
|
||||
|
|
@ -509,8 +515,9 @@ wideP_consurf <- function(plotdf
|
|||
, fill = plotdf[[aa_colour_colname1]]
|
||||
, colour = plotdf[[aa_colour_colname1]]
|
||||
, linetype = "solid")
|
||||
|
||||
if (debug){
|
||||
cat("\nDone Plot with 2 ligands")
|
||||
}
|
||||
}
|
||||
|
||||
#---------------------
|
||||
|
|
@ -519,11 +526,12 @@ wideP_consurf <- function(plotdf
|
|||
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
|
||||
|
|
@ -546,20 +554,20 @@ wideP_consurf <- function(plotdf
|
|||
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")
|
||||
|
||||
, 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")
|
||||
|
|
@ -567,23 +575,23 @@ wideP_consurf <- function(plotdf
|
|||
#==============================================
|
||||
if (A_xvar_lig){
|
||||
legs = cowplot::plot_grid(legend1
|
||||
, legend2
|
||||
, ncol = 1
|
||||
, align = "hv"
|
||||
, rel_heights = c(2/4,3/4))
|
||||
, 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)
|
||||
, 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)
|
||||
, legend1
|
||||
, ncol = 2
|
||||
, align = "hv"
|
||||
, rel_widths = c(9/10, 0.5/10)
|
||||
)
|
||||
}
|
||||
#==============================================
|
||||
|
|
@ -609,9 +617,9 @@ wideP_consurf <- function(plotdf
|
|||
# )
|
||||
# }
|
||||
#==============================================
|
||||
return(out2)
|
||||
#return(out2)
|
||||
|
||||
return(out2)
|
||||
#return(out2)
|
||||
|
||||
}
|
||||
|
||||
#############################################################
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue