refactoring logo plots to add flame bar
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4 changed files with 194 additions and 196 deletions
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@ -1,64 +1,29 @@
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# takes a dataframe and returns the same dataframe with two extra columns for colours and position
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generate_distance_colour_map = function(plotdf,
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generate_distance_colour_map = function(plot_df,
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xvar_colname = "position",
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yvar_colname = 'duet_scaled',
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lig_dist_colname = "ligand_distance",
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lig_dist_colours = c("green", "yellow", "orange", "red"),
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#tpos0 = 0,
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#tpos1 = 0,
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#tpos2 = 0,
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#tpos3 = 0,
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debug = FALSE
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debug = TRUE
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)
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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[[yvar_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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#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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if (debug) {
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cat("\nAnnotating x-axis ~", lig_dist_colname, "requested...")
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}
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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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plot_df['lig_distR'] = round(plot_df[[lig_dist_colname]], digits = 0)
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lig_min = min(round(plot_df[[lig_dist_colname]]), na.rm = T); lig_min
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lig_max = max(round(plot_df[[lig_dist_colname]]), na.rm = T); lig_max
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lig_mean = round(mean(round(plot_df[[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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n_colours = length(sort(unique(round(plot_df[[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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ligD_valsR = sort(unique(round(plot_df[[lig_dist_colname]], digits = 0))); ligD_valsR
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if (debug) {
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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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@ -73,49 +38,49 @@ generate_distance_colour_map = function(plotdf,
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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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if (debug) {
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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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#-------------------------------------
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# merge colour key with plotdf
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# merge colour key with plot_df
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#--------------------------------------
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plotdf = merge(plotdf, ligDcolKey, by = 'lig_distR')
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plot_df = merge(plot_df, 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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return(plotdf)
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# plot_df_check = as.data.frame(cbind(position = plot_df[[xvar_colname]]
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# , ligD = plot_df[[lig_dist_colname]]
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# , ligDR = plot_df$lig_distR
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# , ligD_cols = plot_df$ligD_colours))
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return(plot_df)
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}
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generate_distance_legend = function(plotdf,
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generate_distance_legend = function(plot_df,
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yvar_colname,
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xvar_colname = 'position',
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lig_dist_colname = "ligand_distance",
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legend_title = "Ligand\nDistance"
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)
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)
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{
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# build legend for ligand distance "heat bar"
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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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lig_min = min(round(plot_df[[lig_dist_colname]]), na.rm = T); lig_min
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lig_max = max(round(plot_df[[lig_dist_colname]]), na.rm = T); lig_max
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lig_mean = round(mean(round(plot_df[[lig_dist_colname]]), na.rm = T)); lig_mean
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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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get_legend(ggplot(plotdf, aes_string(x = sprintf("factor(%s)", xvar_colname)
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, y = yvar_colname)) +
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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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, limits = c(lig_min, lig_max)
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, labels = labelsD
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, name = legend_title)
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)
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get_legend(
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ggplot(plot_df, aes_string(x = sprintf("factor(%s)", xvar_colname), y=0)) +
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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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, limits = c(lig_min, lig_max)
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, labels = labelsD
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, name = legend_title)
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)
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}
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@ -54,6 +54,7 @@ lf_bp2 <- function(lf_df = lf_duet
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}else{
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bp_width = bp_width
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}
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my_comparisonsL <- list( stat_grp_comp )
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ggplot(lf_df, aes_string(x = x_grp, y = y_var)) +
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@ -93,39 +94,11 @@ lf_bp2 <- function(lf_df = lf_duet
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, x = ""
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, y = "") +
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if (add_stats){
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my_comparisonsL <- list( stat_grp_comp )
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stat_compare_means(comparisons = my_comparisonsL
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, method = stat_method
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, paired = my_paired
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, label = stat_label[2])
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if (make_boxplot){
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geom_boxplot(fill = "white"
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, outlier.colour = NA
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#, position = position_dodge(width = 0.9)
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, width = bp_width) +
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geom_quasirandom(#priority = "density"
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#, shape = 21
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size = dot_size
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, alpha = dot_transparency
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, show.legend = FALSE
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, cex = 0.8
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, aes(
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colour = factor(
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eval(
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parse(
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text = colour_categ
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)
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)
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)
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)
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)
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} else {
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, label = stat_label[2]) +
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geom_quasirandom(
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size = dot_size
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, alpha = dot_transparency
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@ -142,8 +115,6 @@ lf_bp2 <- function(lf_df = lf_duet
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)
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)
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)
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}
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}
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}
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#lf_bp2(lf_consurf)
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@ -46,7 +46,7 @@ LogoPlotCustomH <- function(plot_df
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, rm_empty_y = F
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, y_axis_log = F
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, log_value = log10
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, y_axis_increment = 5
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, y_axis_increment = 50
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, x_lab = "Position"
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, y_lab = "Odds Ratio"
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, x_ats = 12 # text size
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@ -68,16 +68,24 @@ LogoPlotCustomH <- function(plot_df
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#################################
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# Data processing for logo plot
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#################################
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plot_df = generate_distance_colour_map(plot_df, yvar_colname = y_axis_colname, debug=TRUE)
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plot_df = generate_distance_colour_map(plot_df, debug=TRUE)
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unique_colour_map = unique(plot_df[,c("position","ligD_colours")])
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unique_colour_map = unique_colour_map[order(unique_colour_map$position), ]
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rownames(unique_colour_map) = unique_colour_map$position
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unique_colour_map2 = unique_colour_map
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unique_colour_map2$position=as.factor(unique_colour_map2$position)
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unique_colour_map2$ligD_colours = as.factor(unique_colour_map2$ligD_colours)
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if (rm_empty_y){
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plot_df = plot_df[!is.na(plot_df[y_axis_colname]),]
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cat("\nRemoving empty positions...\n")
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}else{
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plot_df = plot_df
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}
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y_max = max(plot_df['or_mychisq'], na.rm = T)
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y_max = max(plot_df[[y_axis_colname]], na.rm = T)
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cat("\nRemoving y scale incremenet:", y_axis_increment)
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y_lim = round_any(y_max, y_axis_increment, f = ceiling)
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@ -155,50 +163,90 @@ LogoPlotCustomH <- function(plot_df
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y_lab = paste("Log", y_lab)
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}
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}
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ggseqlogo(logo_dfP_wf
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, method = "custom"
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, col_scheme = my_logo_col
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, seq_type = "aa") +
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#ylab("my custom height") +
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theme(axis.text.x = element_text(size = x_ats
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, angle = x_tangle
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, hjust = 1
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, vjust = 0.4
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, colour = xfont_bgc)
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, axis.text.y = element_text(size = y_ats
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, angle = y_tangle
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plot_grid(
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ggplot() +
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geom_logo(logo_dfP_wf
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, method = "custom"
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, col_scheme = my_logo_col
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, seq_type = "aa") +
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#ylab("my custom height") +
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theme( axis.ticks.x = element_blank()
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, axis.title.x = element_blank()
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, axis.text.x = element_blank() # turn this off and the below on if you want to visually
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# verify positions.
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# , axis.text.x = element_text(size = x_ats
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# , angle = x_tangle
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# , hjust = 1
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# , vjust = 0.4
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# , colour = xfont_bgc
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# , margin = margin(b=0)
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# )
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, axis.text.y = element_text(size = y_ats
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, angle = y_tangle
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, hjust = 1
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, vjust = 0
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, colour = yfont_bgc)
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, axis.title.y = element_text(size = y_tts
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, colour = ytt_col)
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, legend.title = element_text(size = leg_tts
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, colour = ytt_col)
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#, legend.text = element_text(size = leg_ts)
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, legend.text = element_blank()
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, legend.position = leg_pos
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, legend.direction = leg_dir
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, plot.background = element_rect(fill = theme_bgc)
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, plot.margin = margin(b=0)
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, panel.grid=element_blank()
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, panel.background = element_rect(fill = theme_bgc)
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)+
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scale_x_discrete(x_lab
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#, breaks
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, labels = position_or
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, limits = factor(1:length(position_or))) +
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scale_y_continuous(y_lab
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, breaks = seq(0, (y_lim), by = y_axis_increment)
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#, labels = seq(0, (y_lim), by = y_axis_increment)
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, limits = c(0, y_lim)) +
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labs(y=y_lab),
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ggplot(data=unique_colour_map2, aes(
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x=factor(position), 0 # heat-mapped distance tiles along the bot
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, fill = position
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, colour = position
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, linetype = "blank"
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)
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) +
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geom_tile() +
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theme(axis.text.x = element_text(size = x_ats
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, angle = x_tangle
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, hjust = 1
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, vjust = 0
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, colour = yfont_bgc)
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, axis.title.x = element_text(size = x_tts
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, colour = xtt_col)
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, axis.title.y = element_text(size = y_tts
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, colour = ytt_col)
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, legend.title = element_text(size = leg_tts
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, colour = ytt_col)
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, legend.text = element_text(size = leg_ts)
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, legend.position = leg_pos
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, legend.direction = leg_dir
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, plot.background = element_rect(fill = theme_bgc))+
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scale_x_discrete(x_lab
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#, breaks
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, labels = position_or
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, limits = factor(1:length(position_or))) +
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scale_y_continuous(y_lab
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, breaks = seq(0, (y_lim), by = y_axis_increment)
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#, labels = seq(0, (y_lim), by = y_axis_increment)
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, limits = c(0, y_lim)) +
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ylab(y_lab) +
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geom_tile(aes(plot_df$position, tpos0 # heat-mapped distance tiles along the bot
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, width = tW0
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, height = tH0)
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, fill = plot_df$ligD_colours
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, colour = plot_df$ligD_colours
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, linetype = "blank")
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#LogoPlot = p0 + ylab(y_lab)
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#return(LogoPlot)
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}
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, vjust = 0.4
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, colour = xfont_bgc)
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, axis.text.y = element_blank()
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, axis.ticks.y = element_blank()
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, axis.title.x = element_text(size = x_tts
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, colour = xtt_col)
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, axis.title.y = element_text(size = y_tts
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, colour = ytt_col)
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, legend.title = element_text(size = leg_tts
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, colour = ytt_col)
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, legend.text = element_text(size = leg_ts)
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, legend.position = leg_pos
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, legend.direction = leg_dir
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, plot.background = element_rect(fill = theme_bgc)
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, plot.margin = margin(t=0)
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, panel.grid=element_blank()
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, panel.background = element_rect(fill = theme_bgc)
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) +
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scale_x_discrete(x_lab, labels=factor(unique_colour_map$position)) +
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scale_color_manual(values=unique_colour_map$ligD_colours) +
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scale_fill_manual(values=unique_colour_map$ligD_colours) +
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labs(y = NULL),
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ncol=1, align='v', rel_heights = c(8/10,1/10)
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)
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}
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#LogoPlotCustomH(merged_df3)
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@ -33,7 +33,7 @@
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LogoPlotSnps <- function(plot_df
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, x_axis_colname = "position"
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, symbol_mut_colname = "mutant_type"
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, symbol_wt_colname = "mutant_type"
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, symbol_wt_colname = "wild_type"
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, omit_snp_count = c(0) # can be 1, 2, etc.
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, my_logo_col = "chemistry"
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, x_lab = "Position"
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@ -66,11 +66,18 @@ LogoPlotSnps <- function(plot_df
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# Generate "ligand distance" colour map
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plot_df = generate_distance_colour_map(plot_df, debug=TRUE)
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unique_colour_map = unique(plot_df[,c("position","ligD_colours")])
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unique_colour_map = unique_colour_map[order(unique_colour_map$position), ]
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rownames(unique_colour_map) = unique_colour_map$position
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unique_colour_map2 = unique_colour_map
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unique_colour_map2$position=as.factor(unique_colour_map2$position)
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unique_colour_map2$ligD_colours = as.factor(unique_colour_map2$ligD_colours)
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#
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setDT(plot_df)[, mut_pos_occurrence := .N, by = .(eval(parse(text=x_axis_colname)))]
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if (debug) {
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table(plot_df[[x_axis_colname]])
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table(plot_df$mut_pos_occurrence)
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table(plot_df[[x_axis_colname]])
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table(plot_df$mut_pos_occurrence)
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}
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max_mut = max(table(plot_df[[x_axis_colname]]))
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@ -200,7 +207,7 @@ LogoPlotSnps <- function(plot_df
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xtt_col = "black"
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ytt_col = "black"
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}
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#####################################
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# Generating logo plots for nsSNPs
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#####################################
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@ -212,11 +219,7 @@ LogoPlotSnps <- function(plot_df
|
|||
, method = 'custom'
|
||||
, col_scheme = my_logo_col
|
||||
, seq_type = 'aa') +
|
||||
|
||||
theme(text=element_text(family="FreeSans"))+
|
||||
theme(axis.text.x = element_blank()) +
|
||||
theme_logo()+
|
||||
|
||||
|
||||
scale_x_continuous(breaks = 1:ncol(tab_mt)
|
||||
, expand = c(0.01,0)
|
||||
, labels = colnames(tab_mt))+
|
||||
|
|
@ -224,16 +227,9 @@ LogoPlotSnps <- function(plot_df
|
|||
scale_y_continuous(breaks = 0:(max_mult_mut-1)
|
||||
, labels = c(1:max_mult_mut)
|
||||
, limits = c(0, max_mult_mut)) +
|
||||
# FIXME: currently broken, possibly due to ggseqlogo() not working in the
|
||||
# way standard ggplot2() does
|
||||
geom_tile(aes(plot_df$position, tpos0 # heat-mapped distance tiles along the bottom.
|
||||
, width = tW0
|
||||
, height = tH0)
|
||||
, fill = plot_df$ligD_colours
|
||||
, colour = plot_df$ligD_colours
|
||||
, linetype = "blank") +
|
||||
ylab(y_lab) +
|
||||
theme(legend.position = leg_pos
|
||||
theme(text=element_text(family="FreeSans")
|
||||
, legend.position = leg_pos
|
||||
, legend.direction = leg_dir
|
||||
, legend.title = element_text(size = leg_tts
|
||||
, colour = ytt_col)
|
||||
|
|
@ -260,40 +256,58 @@ LogoPlotSnps <- function(plot_df
|
|||
, method = 'custom'
|
||||
, col_scheme = my_logo_col
|
||||
, seq_type = 'aa') +
|
||||
|
||||
theme(text = element_text(family="FreeSans"))+
|
||||
theme(axis.text.x = element_blank()
|
||||
, axis.text.y = element_blank()) +
|
||||
theme_logo()+
|
||||
|
||||
scale_x_continuous(breaks = 1:ncol(tab_wt)
|
||||
, expand = c(0.01,0)
|
||||
, labels = colnames(tab_wt))+
|
||||
|
||||
xlab(x_lab) +
|
||||
|
||||
theme(legend.position = "none"
|
||||
, legend.direction = leg_dir
|
||||
#, legend.title = element_blank()
|
||||
, legend.title = element_text(size = y_tts
|
||||
, colour = ytt_col)
|
||||
, legend.text = element_text(size = leg_ts)
|
||||
, axis.text.x = element_text(size = x_ats
|
||||
, angle = x_tangle
|
||||
, hjust = 1
|
||||
, vjust = 0.4
|
||||
, colour = xfont_bgc)
|
||||
theme(text = element_text(family="FreeSans")
|
||||
, legend.position = "none"
|
||||
, axis.text.x = element_blank()
|
||||
, axis.text.y = element_blank()
|
||||
, axis.title.x = element_blank()
|
||||
, axis.title.y = element_blank()
|
||||
, plot.background = element_rect(fill = theme_bgc)
|
||||
) +
|
||||
labs(x=NULL, y=NULL)
|
||||
,
|
||||
ggplot(data=unique_colour_map2, aes(
|
||||
x=factor(position), 0 # heat-mapped distance tiles along the bot
|
||||
, fill = position
|
||||
, colour = position
|
||||
, linetype = "blank"
|
||||
)
|
||||
) +
|
||||
geom_tile() +
|
||||
theme(axis.text.x = element_text(size = x_ats
|
||||
, angle = x_tangle
|
||||
, hjust = 1
|
||||
, vjust = 0.4
|
||||
, colour = xfont_bgc)
|
||||
, axis.text.y = element_blank()
|
||||
, axis.ticks.y = element_blank()
|
||||
, axis.title.x = element_text(size = x_tts
|
||||
, colour = xtt_col)
|
||||
, axis.title.y = element_text(size = y_tts
|
||||
, colour = ytt_col)
|
||||
, legend.title = element_text(size = leg_tts
|
||||
, colour = ytt_col)
|
||||
, legend.text = element_text(size = leg_ts)
|
||||
|
||||
, legend.position = leg_pos
|
||||
, legend.direction = leg_dir
|
||||
, plot.background = element_rect(fill = theme_bgc)
|
||||
)
|
||||
, nrow = 2
|
||||
, plot.margin = margin(t=0)
|
||||
, panel.grid=element_blank()
|
||||
, panel.background = element_rect(fill = theme_bgc)
|
||||
) +
|
||||
scale_x_discrete(x_lab, labels=factor(unique_colour_map$position)) +
|
||||
scale_color_manual(values=unique_colour_map$ligD_colours) +
|
||||
scale_fill_manual(values=unique_colour_map$ligD_colours) +
|
||||
labs(y = NULL)
|
||||
, nrow = 3
|
||||
, align = "v"
|
||||
, rel_heights = c(3/4, 1/4))
|
||||
, rel_heights = c(7/10, 2/7, 1/7))
|
||||
#------------------
|
||||
# Wild logo plot
|
||||
#------------------
|
||||
}
|
||||
#LogoPlotSnps(mutable_df3)
|
||||
|
|
|
|||
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Reference in a new issue