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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,6 @@ | ||
| Package: trackplot | ||
| Title: Generate IGV style track plots and profile plots from bigWig files | ||
| Version: 1.5.10 | ||
| Version: 1.6.00 | ||
| Authors@R: person("Anand", "Mayakonda", , "[email protected]", role = c("aut", "cre")) | ||
| Description: trackplot is an ultra-fast, simple, and minimal dependency R script to generate IGV style track plots (aka locus plots), profile plots and heatmaps from bigWig files. | ||
| License: MIT | ||
|
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@@ -6,6 +6,9 @@ | |
| # Copyright (c) 2020 Anand Mayakonda <[email protected]> | ||
| # | ||
| # Change log: | ||
| # Version: 1.6.00 [2024-10-28] | ||
| # * Added argument `track_overlay` for a single track with line plot. #14 | ||
| # * Bug fix: color alpha differs between tracks. Issue: #34 | ||
| # Version: 1.5.10 [2024-02-14] | ||
| # * Added argument `layout_ord` and `bw_ord` to `track_plot()` re-order the overall tracks and bigWig tracks | ||
| # * Added `xlab` and `ylab` arguments to `profile_plot()` | ||
|
|
@@ -300,6 +303,7 @@ track_summarize = function(summary_list = NULL, condition = NULL, stat = "mean") | |
| #' @param track_names Default NULL | ||
| #' @param track_names_pos Default 0 (corresponds to left corner) | ||
| #' @param track_names_to_left If TRUE, track names are shown to the left of the margin. Default FALSE, plots on top as a title | ||
| #' @param track_overlay Draws all bigWigs in a single track as a line plot | ||
| #' @param regions genomic regions to highlight. A data.frame with at-least three columns containing chr, start and end positions. | ||
| #' @param boxcol color for highlighted region. Default "#192A561A" | ||
| #' @param boxcolalpha Default 0.5 | ||
|
|
@@ -339,10 +343,11 @@ track_plot = function(summary_list = NULL, | |
| track_names = NULL, | ||
| track_names_pos = 0, | ||
| track_names_to_left = FALSE, | ||
| track_overlay = FALSE, | ||
| regions = NULL, | ||
| collapse_txs = TRUE, | ||
| boxcol = "#192A561A", | ||
| boxcolalpha = 0.2, | ||
| boxcol = "#ffc41a", | ||
| boxcolalpha = 0.4, | ||
| chromHMM = NULL, | ||
| chromHMM_cols = NULL, | ||
| chromHMM_names = NULL, | ||
|
|
@@ -469,7 +474,11 @@ track_plot = function(summary_list = NULL, | |
| plot_height_min = round(plot_height_min, digits = 2) | ||
| } | ||
|
|
||
| ntracks = length(summary_list) | ||
| if(is_bw & track_overlay){ | ||
| ntracks = 1 | ||
| }else{ | ||
| ntracks = length(summary_list) | ||
| } | ||
|
|
||
| lo = .make_layout(ntracks = ntracks, ntracks_h = bw_track_height, cytoband = show_ideogram, cytoband_h = cytoband_track_height, genemodel = draw_gene_track, | ||
| genemodel_h = gene_track_height, chrHMM = any(!is.null(ucscChromHMM), !is.null(chromHMM)), chrHMM_h = chromHMM_track_height, loci = !is.null(peaks), | ||
|
|
@@ -526,61 +535,85 @@ track_plot = function(summary_list = NULL, | |
| } | ||
|
|
||
| #Draw bigWig signals | ||
| boxcol = grDevices::adjustcolor(boxcol, alpha.f = boxcolalpha) | ||
| if(is_bw){ | ||
| for(idx in 1:length(summary_list)){ | ||
| x = summary_list[[idx]] | ||
| if(track_overlay){ | ||
|
|
||
| if(show_axis){ | ||
| par(mar = c(0.5, left_mar, 2, 1)) | ||
| }else{ | ||
| par(mar = c(0.5, left_mar, 2, 1)) | ||
| } | ||
|
|
||
| plot(NA, xlim = c(start, end), ylim = c(plot_height_min[idx], plot_height[idx]), frame.plot = FALSE, axes = FALSE, xlab = NA, ylab = NA) | ||
| #If there is no signal, just add the track names and go to next | ||
| if(nrow(x) == 0){ | ||
| if(track_names_to_left){ | ||
| text(x = start, y = 0.5, labels = names(summary_list)[idx], adj = 1, cex = gene_fsize, xpd = TRUE) | ||
| #mtext(text = names(summary_list)[idx], side = 2, line = -2, outer = TRUE, xpd = TRUE, las = 2, adj = 0) | ||
| #title(main = , adj = track_names_pos, font.main = 3) | ||
| }else{ | ||
| title(main = names(summary_list)[idx], adj = track_names_pos, font.main = 3) | ||
| plot(NA, xlim = c(start, end), ylim = c(min(plot_height_min), max(plot_height)), frame.plot = FALSE, axes = FALSE, xlab = NA, ylab = NA) | ||
| for(idx in 1:length(summary_list)){ | ||
| x = summary_list[[idx]] | ||
| if(nrow(x) == 0){ | ||
| if(track_names_to_left){ | ||
| text(x = start, y = 0.5, labels = names(summary_list)[idx], adj = 1, cex = gene_fsize, xpd = TRUE) | ||
| #mtext(text = names(summary_list)[idx], side = 2, line = -2, outer = TRUE, xpd = TRUE, las = 2, adj = 0) | ||
| #title(main = , adj = track_names_pos, font.main = 3) | ||
| }else{ | ||
| title(main = names(summary_list)[idx], adj = track_names_pos, font.main = 3) | ||
| } | ||
| next | ||
| } | ||
| next | ||
| points(x = x$start, y = x$max, col = col[idx], type = "l") | ||
| } | ||
| rect(xleft = x$start, ybottom = 0, xright = x$end, ytop = x$max, col = col[idx], border = col[idx]) | ||
| if(show_axis){ | ||
| axis(side = 2, at = c(plot_height_min[idx], plot_height[idx]), las = 2) | ||
| }else{ | ||
| text(x = start, y = plot_height[idx], labels = paste0("[", plot_height_min[idx], "-", plot_height[idx], "]"), adj = 0, xpd = TRUE) | ||
| } | ||
| #plot(NA, xlim = c(start, end), ylim = c(0, nrow(regions)), frame.plot = FALSE, axes = FALSE, xlab = NA, ylab = NA) | ||
|
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||
| if(plot_regions){ | ||
| # boxcol = "#192a56" | ||
| boxcol = grDevices::adjustcolor(boxcol, alpha.f = boxcolalpha) | ||
| if(nrow(regions) > 0){ | ||
| for(i in 1:nrow(regions)){ | ||
| if(idx == length(summary_list)){ | ||
| #If its a last plot, draw rectangle till 0 | ||
| rect(xleft = regions[i, startpos], ybottom = 0, xright = regions[i, endpos], ytop = plot_height[idx]+10, col = boxcol, border = NA, xpd = TRUE) | ||
| }else if (idx == 1){ | ||
| if(ncol(regions) > 3){ | ||
| text(x = mean(c(regions[i, startpos], regions[i, endpos])), y = plot_height[idx]+(plot_height[idx]*0.1), labels = regions[i, 4], adj = 0.5, xpd = TRUE, font = 1, cex = 1.2) | ||
| }else{ | ||
| text(x = mean(c(regions[i, startpos], regions[i, endpos])), y = plot_height[idx]+(plot_height[idx]*0.1), labels = paste0(regions[i, startpos], "-", regions[i, endpos]), adj = 0.5, xpd = TRUE, font = 1, cex = 1.2) | ||
| } | ||
| rect(xleft = regions[i, startpos], ybottom = -10, xright = regions[i, endpos], ytop = plot_height[idx], col = boxcol, border = NA, xpd = TRUE) | ||
| }else{ | ||
| rect(xleft = regions[i, startpos], ybottom = -10, xright = regions[i, endpos], ytop = plot_height[idx]+10, col = boxcol, border = NA, xpd = TRUE) | ||
| } | ||
| } | ||
| if(nrow(x) > 0){ | ||
| rect(xleft = regions[, startpos], ybottom = 0, xright = regions[, endpos], ytop = max(plot_height), col = boxcol, border = NA, xpd = TRUE) | ||
| } | ||
| } | ||
|
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||
| if(track_names_to_left){ | ||
| text(x = start, y = (plot_height_min[idx] + plot_height[idx])/2, labels = names(summary_list)[idx], adj = 1.1, cex = gene_fsize, xpd = TRUE) | ||
| }else{ | ||
| title(main = names(summary_list)[idx], adj = track_names_pos, font.main = 3) | ||
| if(show_axis){ | ||
| axis(side = 2, at = c(min(plot_height_min), max(plot_height)), las = 2) | ||
| } | ||
| legend(x = "topright", legend = names(summary_list), col = col, pch = "-") | ||
| }else{ | ||
| for(idx in 1:length(summary_list)){ | ||
| x = summary_list[[idx]] | ||
| if(show_axis){ | ||
| par(mar = c(0.5, left_mar, 2, 1)) | ||
| }else{ | ||
| par(mar = c(0.5, left_mar, 2, 1)) | ||
| } | ||
|
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||
| plot(NA, xlim = c(start, end), ylim = c(plot_height_min[idx], plot_height[idx]), frame.plot = FALSE, axes = FALSE, xlab = NA, ylab = NA) | ||
| #If there is no signal, just add the track names and go to next | ||
| if(nrow(x) == 0){ | ||
| if(track_names_to_left){ | ||
| text(x = start, y = 0.5, labels = names(summary_list)[idx], adj = 1, cex = gene_fsize, xpd = TRUE) | ||
| #mtext(text = names(summary_list)[idx], side = 2, line = -2, outer = TRUE, xpd = TRUE, las = 2, adj = 0) | ||
| #title(main = , adj = track_names_pos, font.main = 3) | ||
| }else{ | ||
| title(main = names(summary_list)[idx], adj = track_names_pos, font.main = 3) | ||
| } | ||
| next | ||
| } | ||
| rect(xleft = x$start, ybottom = 0, xright = x$end, ytop = x$max, col = col[idx], border = col[idx]) | ||
|
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||
| if(show_axis){ | ||
| axis(side = 2, at = c(plot_height_min[idx], plot_height[idx]), las = 2) | ||
| }else{ | ||
| text(x = start, y = plot_height[idx], labels = paste0("[", plot_height_min[idx], "-", plot_height[idx], "]"), adj = 0, xpd = TRUE) | ||
| } | ||
| #plot(NA, xlim = c(start, end), ylim = c(0, nrow(regions)), frame.plot = FALSE, axes = FALSE, xlab = NA, ylab = NA) | ||
|
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||
| if(plot_regions){ | ||
| # boxcol = "#192a56" | ||
| if(nrow(x) > 0){ | ||
| rect(xleft = regions[, startpos], ybottom = 0, xright = regions[, endpos], ytop = max(plot_height), col = boxcol, border = NA, xpd = TRUE) | ||
| } | ||
| } | ||
|
|
||
| if(track_names_to_left){ | ||
| text(x = start, y = (plot_height_min[idx] + plot_height[idx])/2, labels = names(summary_list)[idx], adj = 1.1, cex = gene_fsize, xpd = TRUE) | ||
| }else{ | ||
| title(main = names(summary_list)[idx], adj = track_names_pos, font.main = 3) | ||
| } | ||
| } | ||
| } | ||
| }else{ | ||
|
|
@@ -613,20 +646,8 @@ track_plot = function(summary_list = NULL, | |
| # boxcol = "#192a56" | ||
| boxcol = grDevices::adjustcolor(boxcol, alpha.f = boxcolalpha) | ||
| if(nrow(regions) > 0){ | ||
| for(i in 1:nrow(regions)){ | ||
| if(idx == length(summary_list)){ | ||
| #If its a last plot, draw rectangle till 0 | ||
| rect(xleft = regions[i, startpos], ybottom = 0, xright = regions[i, endpos], ytop = plot_height[idx]+10, col = boxcol, border = NA, xpd = TRUE) | ||
| }else if (idx == 1){ | ||
| if(ncol(regions) > 3){ | ||
| text(x = mean(c(regions[i, startpos], regions[i, endpos])), y = plot_height[idx]+(plot_height[idx]*0.1), labels = regions[i, 4], adj = 0.5, xpd = TRUE, font = 1, cex = 1.2) | ||
| }else{ | ||
| text(x = mean(c(regions[i, startpos], regions[i, endpos])), y = plot_height[idx]+(plot_height[idx]*0.1), labels = paste0(regions[i, startpos], "-", regions[i, endpos]), adj = 0.5, xpd = TRUE, font = 1, cex = 1.2) | ||
| } | ||
| rect(xleft = regions[i, startpos], ybottom = -10, xright = regions[i, endpos], ytop = plot_height[idx], col = boxcol, border = NA, xpd = TRUE) | ||
| }else{ | ||
| rect(xleft = regions[i, startpos], ybottom = -10, xright = regions[i, endpos], ytop = plot_height[idx]+10, col = boxcol, border = NA, xpd = TRUE) | ||
| } | ||
| if(nrow(x) > 0){ | ||
| rect(xleft = regions[, startpos], ybottom = 0, xright = regions[, endpos], ytop = max(plot_height), col = boxcol, border = NA, xpd = TRUE) | ||
| } | ||
| } | ||
| } | ||
|
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@@ -1622,8 +1643,11 @@ summarize_homer_annots = function(anno, sample_names = NULL, legend_font_size = | |
|
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||
| ### Re-organize the layout by user specification | ||
| dt = data.table::data.table(name = plot_ord$name, ord = plot_ord$ord, ord_req = plot_ord$ord_req) | ||
|
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||
| dt$n_tracks = ifelse(test = dt$name == 'b', yes = ntracks, no = 1) | ||
| #print(dt) | ||
| dt_s = split(dt, dt$n_tracks) | ||
| #print(dt_s) | ||
| if(length(dt_s) > 1){ | ||
| dt_mult = dt_s[[2]] | ||
| dt_sing = dt_s[[1]] | ||
|
|
@@ -1639,7 +1663,11 @@ summarize_homer_annots = function(anno, sample_names = NULL, legend_font_size = | |
| dt = dt[order(ord_req)] | ||
| data = dt$ord_req4 | ||
| }else{ | ||
| dt = data.table::data.table(name = rep(dt$name, dt$n_tracks), ord = dt$ord, ord_req = dt$ord_req, ord_req2 = seq(dt$ord_req, dt$ord_req + dt$n_tracks -1 , 1), n_tracks = dt$n_tracks) | ||
| #ifelse(test = dt$n_tracks > 1, ) | ||
| #print(dt) | ||
| dt = data.table::data.table(name = rep(dt$name, dt$n_tracks), ord = dt$ord, ord_req = dt$ord_req, ord_req2 = dt$ord_req, n_tracks = dt$n_tracks) | ||
| #print(dt) | ||
|
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| dt = split(dt, dt$ord) |> data.table::rbindlist() | ||
| dt[, ord_req4 := 1:nrow(dt)] | ||
| dt = dt[order(ord_req)] | ||
|
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@@ -1686,6 +1714,8 @@ summarize_homer_annots = function(anno, sample_names = NULL, legend_font_size = | |
| window_dat$chr = chr | ||
| window_dat = window_dat[, .(chr, start, end)] | ||
|
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| print(window_dat) | ||
|
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| op_dir = paste0(op_dir, "/") | ||
|
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||
| if(!dir.exists(paths = op_dir)){ | ||
|
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||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,10 @@ | ||
| bibentry( | ||
| bibtype = "Article", | ||
| title = "Trackplot: a fast and lightweight R script for epigenomic enrichment plots", | ||
| author = personList(as.person("Anand Mayakonda"), | ||
| as.person("Frank Westermann")), | ||
| journal = "Bioinformatics Advances", | ||
| year = "2024", | ||
| volume = "4", | ||
| doi = "doi.org/10.1093/bioadv/vbae031" | ||
| ) |
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