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round_profile.R
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round_profile.R
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#####################################################################
# Rounded CN main method
#####################################################################
create_rounded_copynumber = function(samplename, segments, outdir, method_segmentsfile, method_purityfile, method_baflogr, sex, libpath, max.plot.cn=4, rounding_up=T, make_figures=T) {
#####################################################################
# Read in and map all the raw data
#####################################################################
res = parse_all_profiles(samplename, segments, method_segmentsfile, method_purityfile, method_baflogr, sex)
map_dkfz = res$map_dkfz
map_mustonen = res$map_mustonen
map_peifer = res$map_peifer
map_vanloowedge = res$map_vanloowedge
map_broad = res$map_broad
map_jabba = res$map_jabba
# Calc ploidy of all profiles
ploidy_vanloowedge = get_ploidy(segments, res$map_vanloowedge, libpath)
ploidy_broad = get_ploidy(segments, res$map_broad, libpath, broad=T)
ploidy_peifer = get_ploidy(segments, res$map_peifer, libpath)
ploidy_dkfz = get_ploidy(segments, res$map_dkfz, libpath)
ploidy_mustonen = get_ploidy(segments, res$map_mustonen, libpath)
ploidy_jabba = get_ploidy(segments, res$map_jabba, libpath)
ploidies = data.frame(samplename=samplename,
ploidy_vanloowedge=ploidy_vanloowedge$ploidy, ploidy_broad=ploidy_broad$ploidy, ploidy_peifer=ploidy_peifer$ploidy, ploidy_dkfz=ploidy_dkfz$ploidy, ploidy_mustonen=ploidy_mustonen$ploidy, ploidy_jabba=ploidy_jabba$ploidy,
status_vanloowedge=ploidy_vanloowedge$status, status_broad=ploidy_broad$status, status_peifer=ploidy_peifer$status, status_dkfz=ploidy_dkfz$status, status_mustonen=ploidy_mustonen$status, status_jabba=ploidy_jabba$status)
write.table(ploidies, file=file.path(outdir, "raw_ploidy", paste0(samplename, "_raw_ploidy.txt")), sep="\t", quote=F, row.names=F)
res = parse_all_purities(samplename, method_purityfile)
purity_dkfz = res$dkfz
purity_vanloowedge = res$vanloowedge
purity_broad = res$broad
purity_peifer = res$peifer
purity_mustonen = res$mustonen
purity_jabba = res$jabba
combined_status = get_combined_status(segments, map_vanloowedge, map_dkfz, map_mustonen, map_peifer, map_broad, map_jabba)
#####################################################################
# Make inventory of how many methods call a segment subclonal
#####################################################################
# Exclude mustonen and jabba here as they only report clonal CNA
all_clonal = apply(combined_status[,c("broad", "dkfz", "peifer", "vanloowedge")], 1, function(x) { all(x=="clonal") })
all_clonal[is.na(all_clonal)] = F
all_subclonal = apply(combined_status[,c("broad", "dkfz", "peifer", "vanloowedge")], 1, function(x) { all(x=="subclonal") })
all_subclonal[is.na(all_subclonal)] = F
any_na = apply(combined_status[,c("broad", "dkfz", "peifer", "vanloowedge")], 1, function(x) { any(is.na(x)) })
one_subclonal = apply(combined_status[,c("broad", "dkfz", "peifer", "vanloowedge")], 1, function(x) { sum(x=="subclonal")==1 })
one_subclonal[is.na(one_subclonal)] = F
two_subclonal = apply(combined_status[,c("broad", "dkfz", "peifer", "vanloowedge")], 1, function(x) { sum(x=="subclonal")==2 })
two_subclonal[is.na(two_subclonal)] = F
three_subclonal = apply(combined_status[,c("broad", "dkfz", "peifer", "vanloowedge")], 1, function(x) { sum(x=="subclonal")==3 })
three_subclonal[is.na(three_subclonal)] = F
# sanity check
if (any((all_clonal+all_subclonal+any_na+one_subclonal+two_subclonal+three_subclonal) > 1)) {
print("Found segment with multiple status?")
}
status_inventory = rep(NA, nrow(combined_status))
status_inventory[all_clonal] = "all_clonal"
status_inventory[all_subclonal] = "all_subclonal"
status_inventory[any_na] = "any_na"
status_inventory[one_subclonal] = "one_subclonal"
status_inventory[two_subclonal] = "two_subclonal"
status_inventory[three_subclonal] = "three_subclonal"
combined_status$inventory = status_inventory
write.table(combined_status, file=file.path(outdir, "status_inventory", paste0(samplename, "_status_inventory.txt")), row.names=F, sep="\t", quote=F)
#####################################################################
# Make plots
#####################################################################
if (make_figures) {
print("Making figures")
make_plot = function(mapping, segments, plot_title, max.plot.cn) {
print(plot_title)
if (!is.na(mapping)) {
cn_bb = collapse2bb(segments=segments, cn_states=mapping$cn_states)
} else {
cn_bb = parse_dummy_cn_profile(libpath)
}
plot = plot_profile(cn_bb, plot_title, max.plot.cn=max.plot.cn)
return(plot)
}
plot_vanloowedge = make_plot(map_vanloowedge, segments, "Battenberg", max.plot.cn)
plot_broad = make_plot(map_broad, segments, "ABSOLUTE", max.plot.cn)
plot_dkfz = make_plot(map_dkfz, segments, "ACEseq", max.plot.cn)
plot_mustonen = make_plot(map_mustonen, segments, "CloneHD", max.plot.cn)
plot_peifer = make_plot(map_peifer, segments, "Sclust", max.plot.cn)
plot_jabba = make_plot(map_peifer, segments, "JaBbA", max.plot.cn)
print("Done plot profile")
png(file.path(outdir, "figures", paste0(samplename, "_copynumber_complete.png")), height=1700, width=1300)
grid.arrange(arrangeGrob(plot_broad, plot_dkfz, plot_vanloowedge, plot_mustonen, plot_peifer, plot_jabba, ncol=1),
top=textGrob(samplename, gp = gpar(fontsize=25, face=2, col="black")))
dev.off()
}
#####################################################################
# Make rounded clonal copy number
#####################################################################
print("Rounding segments")
rounded_clonal = list(broad=data.frame(), dkfz=data.frame(), vanloowedge=data.frame(), peifer=data.frame(), mustonen=data.frame(), jabba=data.frame())
for (i in 1:nrow(segments)) {
if (!is.na(map_broad) && length(map_broad$cn_states) >= i) {
rounded_clonal$broad = rbind(rounded_clonal$broad, round_broad(map_broad, i, rounding_up=rounding_up))
} else {
temp_entry = get_dummy_cn_entry(segments[i,,drop=F])
temp_entry$historically_clonal = 0
rounded_clonal$broad = rbind(rounded_clonal$broad, temp_entry)
}
if (!is.na(map_vanloowedge) && length(map_vanloowedge$cn_states) >= i) {
rounded_clonal$vanloowedge = rbind(rounded_clonal$vanloowedge, round_vanloo_wedge(map_vanloowedge, i, purity_vanloowedge, rounding_up=rounding_up))
} else {
temp_entry = get_dummy_cn_entry(segments[i,,drop=F])
colnames(temp_entry)[7] = "cellular_prevalence"
temp_entry$ccf = NA
rounded_clonal$vanloowedge = rbind(rounded_clonal$vanloowedge, temp_entry)
}
if (!is.na(map_peifer) && length(map_peifer$cn_states) >= i) {
rounded_clonal$peifer = rbind(rounded_clonal$peifer, round_peifer(map_peifer, i, purity_peifer, rounding_up=rounding_up))
} else {
temp_entry = get_dummy_cn_entry(segments[i,,drop=F])
colnames(temp_entry)[7] = "cellular_prevalence"
temp_entry$ccf = NA
rounded_clonal$peifer = rbind(rounded_clonal$peifer, temp_entry)
}
if (!is.na(map_mustonen) && length(map_mustonen$cn_states) >= i) {
rounded_clonal$mustonen = rbind(rounded_clonal$mustonen, round_mustonen(map_mustonen, i))
} else {
temp_entry = get_dummy_cn_entry(segments[i,,drop=F])
colnames(temp_entry)[7] = "cellular_prevalence"
temp_entry$ccf = NA
rounded_clonal$mustonen = rbind(rounded_clonal$mustonen, temp_entry)
}
if (!is.na(map_dkfz) && length(map_dkfz$cn_states) >= i) {
rounded_clonal$dkfz = rbind(rounded_clonal$dkfz, round_dkfz(map_dkfz, i, purity_dkfz, rounding_up=rounding_up))
} else {
temp_entry = get_dummy_cn_entry(segments[i,,drop=F])
colnames(temp_entry)[7] = "cellular_prevalence"
temp_entry$dh = 0
temp_entry$covRatio = 0
temp_entry$ccf = NA
rounded_clonal$dkfz = rbind(rounded_clonal$dkfz, temp_entry)
}
if (!is.na(map_jabba) && length(map_jabba$cn_states) >= i) {
rounded_clonal$jabba = rbind(rounded_clonal$jabba, round_jabba(map_jabba, i))
} else {
temp_entry = get_dummy_cn_entry(segments[i,,drop=F])
colnames(temp_entry)[7] = "cellular_prevalence"
temp_entry$ccf = NA
rounded_clonal$jabba = rbind(rounded_clonal$jabba, temp_entry)
}
}
print("Calling unique")
for (i in 1:length(rounded_clonal)) {
rounded_clonal[[i]] = unique(rounded_clonal[[i]])
}
print("Writing data to file")
# write out the complete profiles
for (i in 1:length(rounded_clonal)) {
cn_method = names(rounded_clonal)[i]
if (rounding_up) {
dir_postfix = paste0(cn_method, "_rounded_clonal")
} else {
dir_postfix = paste0(cn_method, "_rounded_alt_clonal")
}
write.table(rounded_clonal[[i]], file=file.path(outdir, dir_postfix, paste0(samplename, "_segments.txt")), quote=F, sep="\t", row.names=F)
}
#####################################################################
# Plot rounded clonal
#####################################################################
if (make_figures) {
print("Making figures - rounded")
print("Battenberg")
cn_bb_vanloowedge = collapseRoundedClonal2bb(cn_states=rounded_clonal$vanloowedge, libpath=libpath)
plot_vanloowedge = plot_profile(cn_bb_vanloowedge, "Battenberg", max.plot.cn=max.plot.cn)
print("ABSOLUTE")
cn_bb_broad = collapseRoundedClonal2bb(cn_states=rounded_clonal$broad, libpath=libpath)
plot_broad = plot_profile(cn_bb_broad, "ABSOLUTE", max.plot.cn=max.plot.cn)
print("ACEseq")
cn_bb_dkfz = collapseRoundedClonal2bb(cn_states=rounded_clonal$dkfz, libpath=libpath)
plot_dkfz = plot_profile(cn_bb_dkfz, "ACEseq", max.plot.cn=max.plot.cn)
print("CloneHD")
cn_bb_mustonen = collapseRoundedClonal2bb(cn_states=rounded_clonal$mustonen, libpath=libpath)
plot_mustonen = plot_profile(cn_bb_mustonen, "CloneHD", max.plot.cn=max.plot.cn)
print("Sclust")
cn_bb_peifer = collapseRoundedClonal2bb(cn_states=rounded_clonal$peifer, libpath=libpath)
plot_peifer = plot_profile(cn_bb_peifer, "Sclust", max.plot.cn=max.plot.cn)
print("JaBbA")
cn_bb_jabba = collapseRoundedClonal2bb(cn_states=rounded_clonal$jabba, libpath=libpath)
plot_jabba = plot_profile(cn_bb_jabba, "JaBbA", max.plot.cn=max.plot.cn)
png(file.path(outdir, "figures", paste0(samplename, "_copynumber_rounded_clonal.png")), height=1700, width=1300)
grid.arrange(arrangeGrob(plot_broad, plot_dkfz, plot_vanloowedge, plot_mustonen, plot_peifer, plot_jabba, ncol=1),
top=textGrob(samplename, gp = gpar(fontsize=25, face=2, col="black")))
dev.off()
}
}
#####################################################################
# Script
#####################################################################
#' TODO
#' - File paths at the top of the create_rounded_copynumber could be improved, maybe move all the input into an input directory
args = commandArgs(T)
libpath = args[1]
samplename = args[2]
outdir = args[3]
rounding_up = as.logical(args[4])
make_figures = as.logical(args[5])
sex = args[6]
source(file.path(libpath, "util.R"))
# setwd("/Users/sd11/Documents/Projects/icgc/consensus_subclonal_copynumber/6aa00162-6294-4ce7-b6b7-0c3452e24cd6")
# setwd("/nfs/users/nfs_c/cgppipe/pancancer/workspace/sd11/icgc_pancan_full/consensus_copynumber/2016_09_consensus_breakpoints_fullruns/20161024_rounding/")
# samplename = "6aa00162-6294-4ce7-b6b7-0c3452e24cd6"
# setwd("/Users/sd11/Documents/Projects/icgc/consensus_subclonal_copynumber/final_run_testing")
# samplename = "003819bc-c415-4e76-887c-931d60ed39e7"
# sex = "female"
# outdir = "output"
data_bundle_profiles_path = "data_bundle/input_profiles/"
dkfz_segmentsfile = file.path(data_bundle_profiles_path, paste0("dkfz/segments/", samplename, "_segments.txt"))
dkfz_purityfile = file.path(data_bundle_profiles_path, paste0("dkfz/purity_ploidy.txt"))
vanloowedge_segmentsfile = file.path(data_bundle_profiles_path, paste0("vanloo_wedge/segments/", samplename, "_segments.txt"))
vanloowedge_purityfile = file.path(data_bundle_profiles_path, paste0("vanloo_wedge/purity_ploidy.txt"))
peifer_segmentsfile = file.path(data_bundle_profiles_path, paste0("peifer/segments/", samplename, "_segments.txt"))
peifer_purityfile = file.path(data_bundle_profiles_path, paste0("peifer/purity_ploidy.txt"))
#mustonen_segmentsfile = paste0("mustonen/", samplename, ".penalty0.95_segments.txt")
mustonen_segmentsfile = file.path(data_bundle_profiles_path, paste0("mustonen/segments/", samplename, "_segments.txt"))
mustonen_purityfile = file.path(data_bundle_profiles_path, paste0("mustonen/purity_ploidy.txt"))
jabba_segmentsfile = file.path(data_bundle_profiles_path, paste0("jabba/segments/", samplename, "_segments.txt"))
jabba_purityfile = file.path(data_bundle_profiles_path, paste0("jabba/purity_ploidy.txt"))
broad_segmentsfile = file.path(data_bundle_profiles_path, paste0("broad/segments/", samplename, "_segments.txt"))
broad_purityfile = file.path(data_bundle_profiles_path, paste0("broad/purity_ploidy.txt"))
vanloowedge_baflogrfile = file.path(data_bundle_profiles_path, paste0("vanloo_wedge/baflogr/", samplename, "_baflogr.txt"))
broad_baflogrfile = file.path(data_bundle_profiles_path, paste0("broad/baflogr/", samplename, "_baflogr.txt"))
method_segmentsfile = list(dkfz=dkfz_segmentsfile,
vanloowedge=vanloowedge_segmentsfile,
peifer=peifer_segmentsfile,
mustonen=mustonen_segmentsfile,
broad=broad_segmentsfile,
jabba=jabba_segmentsfile)
method_purityfile = list(dkfz=dkfz_purityfile,
vanloowedge=vanloowedge_purityfile,
peifer=peifer_purityfile,
mustonen=mustonen_purityfile,
broad=broad_purityfile,
jabba=jabba_purityfile)
method_baflogr = list(vanloowedge=vanloowedge_baflogrfile,
broad=broad_baflogrfile)
breakpoints_file = file.path("data_bundle/consensus_breakpoints", paste0(samplename, ".txt"))
if (file.exists(breakpoints_file)) {
breakpoints = read.table(breakpoints_file, header=T, stringsAsFactors=F)
segments = breakpoints2segments(breakpoints)
create_rounded_copynumber(samplename,
segments,
outdir,
method_segmentsfile,
method_purityfile,
method_baflogr,
sex,
libpath=libpath,
max.plot.cn=4,
rounding_up=rounding_up,
make_figures=make_figures)
}
q(save="no")
# 02917220-6a7a-46a1-8656-907e96bef88e output/ TRUE FALSE male