Mercurial > repos > greg > ideas_genome_tracks
changeset 42:102593f75a8d draft
Uploaded
| author | greg |
|---|---|
| date | Wed, 13 Dec 2017 11:11:09 -0500 |
| parents | 8fee8b633db6 |
| children | bb6523f6eec5 |
| files | ideas_genome_tracks.R |
| diffstat | 1 files changed, 102 insertions(+), 63 deletions(-) [+] |
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--- a/ideas_genome_tracks.R Wed Dec 13 11:11:02 2017 -0500 +++ b/ideas_genome_tracks.R Wed Dec 13 11:11:09 2017 -0500 @@ -15,33 +15,13 @@ make_option(c("--output_trackhub"), action="store", dest="output_trackhub", help="Output hub file"), make_option(c("--output_trackhub_files_path"), action="store", dest="output_trackhub_files_path", help="Output hub extra files path"), make_option(c("--output_trackhub_id"), action="store", dest="output_trackhub_id", help="Encoded output_trackhub dataset id"), - make_option(c("--short_label"), action="store", dest="short_label", help="Hub short label"), - make_option(c("--track_color"), action="store", dest="track_color", default=NULL, help="User specified track color") + make_option(c("--short_label"), action="store", dest="short_label", help="Hub short label") ) parser <- OptionParser(usage="%prog [options] file", option_list=option_list) args <- parse_args(parser, positional_arguments=TRUE) opt <- args$options -create_color_scheme = function(input_dir_para) { - # Create the color scheme. - para_files <- list.files(path=input_dir_para, full.names=TRUE); - mc = NULL; - x = read.table(para_files[1], comment="!", nrows=1); - l = as.integer(regexpr("\\*", as.matrix(x))); - l = min(which(l>0)) - 2; - x = as.matrix(read.table(para_files[1])); - if (length(para_files) > 1) { - for (i in 2:length(para_files)) { - x = x + as.matrix(read.table(para_files[i])); - } - } - p = x[,1] / sum(x[,1]); - m = array(as.matrix(x[,1:l+1] / x[,1]), dim=c(dim(x)[1], l)); - track_color <- get_track_color(m, mc); - return(track_color); -} - create_primary_html = function(output_trackhub, tracks_dir, build) { track_files <- list.files(path=tracks_dir); s <- paste('<html><head></head><body>', sep="\n"); @@ -54,7 +34,8 @@ cat(s, file=output_trackhub); } -create_track = function(input_dir_state, chrom_len_file, base_track_file_name, track_color) { +create_track = function(input_dir_para, input_dir_state, chrom_len_file, base_track_file_name) { + para_files <- list.files(path=input_dir_para, full.names=TRUE); state_files <- list.files(path=input_dir_state, full.names=TRUE); genome_size = read.table(chrom_len_file); g = NULL; @@ -94,15 +75,16 @@ tt = c(tt, which(posst[2:L]!=posed[2:L-1])); tt = sort(unique(tt)); for(i in 1:n) { + state_color <- get_state_color(para_files[i]) tstate = state[,i]; t = c(tt, which(tstate[2:L]!=tstate[2:L-1])); t = sort(unique(t)); t0 = c(0, t) + 1; t = c(t, L); np = cbind(chr[t], posst[t0], posed[t], tstate[t]); - x = cbind(np[,1:3], state_name[as.integer(np[,4])+1], 1000, ".", np[,2:3], track_color[as.numeric(np[,4])+1]); track_file_name_bed <- get_track_file_name(base_track_file_name, i, "bed"); track_file_name_bigbed <- get_track_file_name(base_track_file_name, i, "bigbed"); + x = cbind(np[, 1:3], state_name[as.integer(np[,4])+1], 1000, ".", np[,2:3], state_color[as.numeric(np[,4])+1]); write.table(as.matrix(x), track_file_name_bed, quote=F, row.names=F, col.names=F); system(paste("bedToBigBed ", track_file_name_bed, chrom_len_file, " ", track_file_name_bigbed)); system(paste("rm ", track_file_name_bed)); @@ -110,9 +92,9 @@ return(cells); } -create_track_db = function(galaxy_url, encoded_dataset_id, input_dir_state, build, chrom_len_file, tracks_dir, hub_name, short_label, long_label, track_color) { +create_track_db = function(galaxy_url, encoded_dataset_id, input_dir_para, input_dir_state, build, chrom_len_file, tracks_dir, hub_name, short_label, long_label) { base_track_file_name <- paste(tracks_dir, hub_name, sep=""); - cells = create_track(input_dir_state, chrom_len_file, base_track_file_name, track_color); + cells = create_track(input_dir_para, input_dir_state, chrom_len_file, base_track_file_name); cell_info = cbind(cells, cells, cells, "#000000"); cell_info = array(cell_info, dim=c(length(cells), 4)); cell_info = as.matrix(cell_info); @@ -146,58 +128,115 @@ return(s) } -get_hue = function(val, min=0, max=1) { - if (is.null(val)) { - val = max; - } else if (is.na(val)) { - val = max; - } else if (val < min) { - val = min; - } else if (val > max) { - val = max; - } - return(val); -} - -get_track_color = function(statemean, markcolor=NULL) { - sm_width = dim(statemean)[1]; - sm_height = dim(statemean)[2]; - if (length(markcolor) == 0) { - markcolor = rep("", sm_height); - markcolor[order(apply(statemean, 2, sd), decreasing=T)] = hsv((1:sm_height-1)/sm_height, 1, 1); +get_rgb<-function(statemean, markcolor=NULL) +{ + if(length(markcolor) == 0) { + markcolor = rep("",dim(statemean)[2]); + markcolor[order(apply(statemean,2,sd),decreasing=T)]=hsv((1:dim(statemean)[2]-1)/dim(statemean)[2],1,1) markcolor = t(col2rgb(markcolor)); } + rg = apply(statemean, 1, range); mm = NULL; - for (i in 1:sm_width) { - mm = rbind(mm, statemean[i,] - rg[1,i] + 1e-10 / rg[2,i] - rg[1,i] + 1e-10); + for(i in 1:dim(statemean)[1]) { + mm = rbind(mm, (statemean[i,]-rg[1, i]+1e-10)/(rg[2, i]-rg[1, i]+1e-10)); } - mm = mm^6; - if(dim(mm)[2] > 1) { - mm = mm / (apply(mm, 1, sum) + 1e-10); + mm = mm^5; + if (dim(mm)[2]>1) { + mm = mm / (apply(mm, 1, sum)+1e-10); } mycol = mm%*%markcolor; s = apply(statemean, 1, max); - s = (s - min(s)) / (max(s) - min(s) + 1e-10); - h = t(apply(mycol, 1, function(x) {rgb2hsv(r=get_hue(x[1]), g=get_hue(x[2]), b=get_hue(x[3]))})); - h[,2] = h[,2] * s; - h = apply(h, 1, function(x) {hsv(x[1], x[2], x[3])}); - rt = cbind(apply(t(col2rgb(h)), 1, function(x) {paste(x, collapse=",")}), h); + s = (s-min(s))/(max(s)-min(s)+1e-10); + mycol = round(255-(255-mycol)*s/0.5); + mycol[mycol<0] = 0; + rt = paste(mycol[,1], mycol[,2], mycol[,3], sep=","); + h = t(apply(mycol, 1, function(x){rgb2hsv(x[1], x[2], x[3])})); + h = apply(h, 1, function(x){hsv(x[1], x[2], x[3])}); + rt = cbind(rt, h); + return(rt); + + h = t(apply(mycol, 1, function(x){rgb2hsv(x[1], x[2], x[3])})); + h[,2] = h[,2]*s; + h = apply(h, 1, function(x){hsv(x[1], x[2], x[3])}); + rt = cbind(apply(t(col2rgb(h)), 1, function(x){paste(x, collapse=",")}), h); return(rt); } +get_state_color <- function(para_file, cols=c("white", "dark blue")) { + x = read.table(parafile, comment.char="#", header=T); + k = dim(x)[2]; + l = dim(x)[1]; + p = (sqrt(9+8*(k-1))-3)/2; + m = as.matrix(x[,1+1:p]/x[,1]); + colnames(m) = colnames(x)[1+1:p]; + marks = colnames(m); + rownames(m) = paste(1:l-1," (",round(x[,1]/sum(x[,1])*10000)/100,"%)",sep=""); + par(mar=c(6,1,1,6)); + rg = range(m); + colors = 0:100/100*(rg[2]-rg[1])+rg[1]; + my_palette = colorRampPalette(cols)(n=100); + defpalette = palette(my_palette); + plot(NA,NA,xlim=c(0,p+0.7),ylim=c(0,l),xaxt="n",yaxt="n",xlab=NA,ylab=NA,frame.plot=F); + axis(1,at=1:p-0.5,labels=colnames(m),las=2); + axis(4,at=1:l-0.5,labels=rownames(m),las=2); + rect(rep(1:p-1,l),rep(1:l-1,each=p),rep(1:p,l),rep(1:l,each=p),col=round((t(m)-rg[1])/(rg[2]-rg[1])*100)); + markcolor = t(col2rgb(terrain.colors(ceiling(p))[1:p])); + for(i in 1:length(marks)) { + if (regexpr("h3k4me3",tolower(marks[i]))>0) { + markcolor[i,]=c(255,0,0); + } + if (regexpr("h3k4me2",tolower(marks[i]))>0) { + markcolor[i,]=c(250,100,0); + } + if (regexpr("h3k4me1",tolower(marks[i]))>0) { + markcolor[i,]=c(250,250,0); + } + if (regexpr("h3k36me3",tolower(marks[i]))>0) { + markcolor[i,]=c(0,150,0); + } + if (regexpr("h2a",tolower(marks[i]))>0) { + markcolor[i,]=c(0,150,150); + } + if (regexpr("dnase",tolower(marks[i]))>0) { + markcolor[i,]=c(0,200,200); + } + if (regexpr("atac",tolower(marks[i]))>0) { + markcolor[i,]=c(0,200,200); + } + if (regexpr("h3k9ac",tolower(marks[i]))>0) { + markcolor[i,]=c(250,0,200); + } + if (regexpr("h3k9me3",tolower(marks[i]))>0) { + markcolor[i,]=c(100,100,100); + } + if (regexpr("h3k27ac",tolower(marks[i]))>0) { + markcolor[i,]=c(250,150,0); + } + if (regexpr("h3k27me3",tolower(marks[i]))>0) { + markcolor[i,]=c(0,0,225); + } + if (regexpr("h3k79me2",tolower(marks[i]))>0) { + markcolor[i,]=c(200,0,200); + } + if (regexpr("h4k20me1",tolower(marks[i]))>0) { + markcolor[i,]=c(50,200,50); + } + if (regexpr("ctcf",tolower(marks[i]))>0) { + markcolor[i,]=c(200,0,250); + } + } + statecolor = get_rgb(m, markcolor)[,]; + rect(rep(p+0.2,l),1:l-0.8,rep(p+0.8,l),1:l-0.2,col=statecolor[,2]); + palette(defpalette); + return(statecolor); +} + get_track_file_name = function(base_track_file_name, index, ext) { track_file_name <- paste(base_track_file_name, index, ext, sep="."); return(track_file_name); } -# Create the color scheme. -if (length(opt$track_color) == 0) { - track_color <- create_color_scheme(opt$input_dir_para); -} else { - track_color <- col2rgb(opt$track_color); -} - # Create the hub.txt output. hub_name_line <- paste("hub ", opt$hub_name, sep=""); short_label_line <- paste("shortLabel ", opt$short_label, sep=""); @@ -220,11 +259,11 @@ # Create the tracks. tracks_dir <- paste(hub_dir, opt$build, "/", sep=""); dir.create(tracks_dir, showWarnings=FALSE); -track_db <- create_track_db(opt$galaxy_url, opt$output_trackhub_id, opt$input_dir_state, opt$build, opt$chrom_len_file, tracks_dir, opt$hub_name, opt$short_label, opt$long_label, track_color); +track_db <- create_track_db(opt$galaxy_url, opt$output_trackhub_id, opt$input_dir_para, opt$input_dir_state, opt$build, opt$chrom_len_file, tracks_dir, opt$hub_name, opt$short_label, opt$long_label); # Create the trackDb.txt output. track_db_file_path <- paste(tracks_dir, "trackDb.txt", sep=""); write.table(track_db, file=track_db_file_path, quote=F, row.names=F, col.names=F); # Create the primary HTML dataset. -create_primary_html(opt$output_trackhub, tracks_dir, opt$build); \ No newline at end of file +create_primary_html(opt$output_trackhub, tracks_dir, opt$build);