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auxiliary_trackhubs_functions.R
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auxiliary_trackhubs_functions.R
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#!/usr/bin/R
# ---------------------------------
# Functions for creating trackhubs:
# ---------------------------------
make.ucsc = function(sdf){
# Make subtrack metadata:
sdf$track = paste0("track BW_", sdf$id, "_", sdf$mark,"_", substr(sdf$dataset,1,3))
sdf$shortLabel = paste("shortLabel", substr(sdf$dataset,1,3), sdf$infoline)
sdf$longLabel = paste0("longLabel ", sdf$id, " ", sdf$mark, " ", sdf$name, ' (', sdf$dataset, ')')
sdf$bigDataUrl = paste0('bigDataUrl ', sdf$dir, sdf$prefix, '.bigWig')
sdf$attr = paste(c("type bigWig 0 30",
"viewLimits 0.0:30.0",
"noInherit on",
"autoScale on",
"yLineOnOff on",
"maxHeightPixels 64:32:16",
"priority 1"), collapse='\n')
sdf$color = sapply(sdf$COLOR, function(x){x = col2rgb(x); paste0('color ',x[1], ',', x[2],',', x[3])})
sdf$metadata = paste('metadata',
paste0('"Epigenome ShortName"="', sdf$infoline,'"'),
paste0('"Epigenome FullName"="', sdf$name,'"'),
paste0('"Group"="<span style="color:', sdf$COLOR,'">', sdf$GROUP, '</span>"'),
paste0('"Type"="', sdf$type,'"'),
paste0('"Sex"="', sdf$sex,'"'),
# paste0('"Age"="', sdf$fullage,'"'),
paste0('"Donor"="', sdf$Donor,'"'),
sep=" ")
sdf$subGroups = paste0('subGroups view=Sig sampleType=', sdf$id, ' assayType=', sdf$mark, ' dataType=', sdf$dataset, ' donor=', sdf$Donor)
sdf$parent = paste0('parent EpiMapBWSigView off')
track.meta = paste(sdf$track, sdf$shortLabel, sdf$longLabel, sdf$bigDataUrl,
sdf$attr, sdf$color, sdf$metadata, sdf$subGroups, sdf$parent, sep="\n")
# Assays and donors:
adf = aggregate(id ~ mark, sdf, length)
adf = adf[order(adf$id, decreasing=T),]
atypes = adf$mark
ddf = aggregate(id ~ Donor, sdf, length)
ddf = ddf[order(ddf$id, decreasing=T),]
dtypes = ddf$Donor
idf = unique(sdf[,c('id','ct')])
idf$ctspace = gsub(" ","_", idf$ct)
# Overall metadata:
ovl.meta = c('track EpiMapBWSig',
'compositeTrack on',
'shortLabel All Signal Tracks',
'longLabel All observed and imputed signal tracks from EpiMap',
'group epimap',
'subGroup1 view Views Sig=Signal',
paste(c('subGroup2 sampleType Sample_Type', paste0(idf$id, '=', idf$ctspace)), collapse=' '),
paste(c('subGroup3 assayType Assay_Type ', paste0(atypes, '=', atypes)), collapse=' '),
'subGroup4 dataType Data_Type Observed=Observed Imputed=Imputed',
paste(c('subGroup5 donor Donor ', paste0(dtypes, '=', dtypes)), collapse=' '),
'dimensions dimensionX=assayType dimensionY=sampleType dimA=dataType dimB=donor',
'filterComposite on',
'sortOrder cellType=+ assayType=+ donor=+',
'dragAndDrop on',
'visibility hide',
'priority 21',
'type bed 3',
'noInherit on')
# View track:
view.meta = c('track EpiMapBWSigView',
'shortLabel Signal',
'view Sig',
'maxHeightPixels 64:32:16',
'parent EpiMapBWSig',
'type bigWig',
'visibility dense')
# Hub description; use one file for the full hub:
hub.meta = c('hub EpiMapCustom',
'shortLabel EpiMap release v0.9 (Custom TrackHub)',
'longLabel Custom trackHub per mark and sample group tracks for EpiMap v0.9',
'useOneFile on',
'email [email protected]',
'\n',
'genome hg19')
hub.line = paste(hub.meta, collapse='\n')
ovl.line = paste(ovl.meta, collapse='\n')
view.line = paste(view.meta, collapse='\n')
track.line = paste(track.meta, collapse='\n\n')
ucschub = c(hub.line, ovl.line, view.line, track.line)
ucschub = paste(ucschub, collapse='\n\n')
return(ucschub)
}
# TODO: Can we automatically make data go into a dense visualization if more than X tracks
# TODO: Allow choosing track color by datatype, group, (lifestage, etc must be careful with grey/unknown.)
make.legacy.wustl = function(sdf){
sdf$colorstr = sapply(sdf$COLOR, function(x){x = col2rgb(x); paste0('"pr": ',x[1], ', "pg": ', x[2],', "pb": ', x[3])})
# Base string attributes:
base.info = '{"type": "native_track", "list": [{"name": "refGene" ,"mode":"full"}]}, {"type":"coordinate_override","coord":"chr9,36329955,chr9,37537411"}'
# TODO: make the metadata definitions:
# Make the per-mark strings:
sdf$trackline = paste0("{", paste0('"name": "', substr(sdf$dataset,1,3), " ", sdf$id, " ", sdf$mark,' (', sdf$ct, ')", '),
# sdf$trackline = paste0("{", paste0('"name": "', substr(sdf$dataset,1,3), " ", sdf$id, " ", sdf$mark,'", '),
paste0('"url": "', sdf$dir, sdf$prefix, '.bigWig", '),
'"type": "bigwig", "height": 30, "mode":1, "qtc":{"anglescale":1, "height":30, "summeth":2, "thtype":1, "thmin":0, "thmax":20, "smooth":3,',
sdf$colorstr, '}',
', "metadata": {',
paste0('"Assay": "', sdf$mark,'", '),
paste0('"Sample": "', sdf$ct,'", '),
paste0('"Group": "', sdf$GROUP,'", '),
paste0('"Lifestage": "', sdf$lifestage,'", '),
paste0('"Sex": "', sdf$sex,'", '),
paste0('"Type": "', sdf$type,'"'),"},",
paste0('"options": {"color": "', sdf$COLOR, '"}'),
"}")
json.line = paste("[", base.info, ",\n ", paste(sdf$trackline, collapse=",\n "), "]")
return(json.line)
}