R/cgdsr.R
In cBioPortal/cgdsr: R-Based API for Accessing the MSKCC Cancer Genomics Data Server (CGDS)
Defines functions
.onAttach
library(R.oo)
.onAttach <- function(libname, pkgname){
packageStartupMessage('Please send questions to cbioportal@googlegroups.com')
}
setConstructorS3("CGDS", function(url='',verbose=FALSE,ploterrormsg='',token=NULL) {
extend(Object(), "CGDS",
.url=url,
.token=token,
.verbose=verbose,
.ploterrormsg='')
})
setMethodS3("processURL","CGDS", private=TRUE, function(x, url, force.comment.char.blank=FALSE, ...) {
if (x$.verbose) cat(url,"\n")
headers <- httr::add_headers()
if(!is.null(x$.token)) {
headers <- httr::add_headers(Authorization = paste("Bearer ", x$.token, sep = ""))
}
r <- httr::GET(url, headers)
httr::stop_for_status(r)
if(force.comment.char.blank) {
df = read.table(skip=0, header=TRUE, as.is=TRUE, sep="\t", quote='', comment.char='', fill=TRUE, text=httr::content(r, "text"))
} else {
df = read.table(skip=0, header=TRUE, as.is=TRUE, sep="\t", quote='', fill=TRUE, text=httr::content(r, "text"))
}
})
setMethodS3("setPlotErrorMsg","CGDS", function(x, msg, ...) {
x$.ploterrormsg = msg
return(msg)
})
setMethodS3("setVerbose","CGDS", function(x, verbose, ...) {
x$.verbose = verbose
return(verbose)
})
setMethodS3("getCancerStudies","CGDS", function(x, ...) {
url = paste(x$.url, "webservice.do?cmd=getCancerStudies&",sep="")
df = processURL(x,url)
return(df)
})
setMethodS3("getCaseLists","CGDS", function(x, cancerStudy, ...) {
url = paste(x$.url, "webservice.do?cmd=getCaseLists&cancer_study_id=", cancerStudy, sep="")
df = processURL(x,url)
return(df)
})
setMethodS3("getGeneticProfiles","CGDS", function(x, cancerStudy, ...) {
url = paste(x$.url, "webservice.do?cmd=getGeneticProfiles&cancer_study_id=", cancerStudy, sep="")
df = processURL(x,url)
return(df)
})
setMethodS3("getMutationData","CGDS", function(x, caseList, geneticProfile, genes, ...) {
url = paste(x$.url, "webservice.do?cmd=getMutationData",
"&case_set_id=", caseList,
"&genetic_profile_id=", geneticProfile,
"&gene_list=", paste(genes,collapse=","), sep="")
df = processURL(x,url)
return(df)
})
setMethodS3("getProfileData","CGDS", function(x, genes, geneticProfiles, caseList='', cases=c(), caseIdsKey = '', ...) {
url = paste(x$.url, "webservice.do?cmd=getProfileData",
"&gene_list=", paste(genes,collapse=","),
"&genetic_profile_id=", paste(geneticProfiles,collapse=","),
"&id_type=", 'gene_symbol',
sep="")
if (length(cases)>0) { url = paste(url,"&case_list=", paste(cases,collapse=","),sep='')
} else if (caseIdsKey != '') { url = paste(url,"&case_ids_key=", caseIdsKey,sep='')
} else { url = paste(url,"&case_set_id=", caseList,sep='') }
df = processURL(x,url)
if (nrow(df) == 0) { return(df) }
m = matrix()
# process data before returning
if (length(geneticProfiles) > 1) {
cnames = df[,1]
m = t(df[,-c(1:4)])
colnames(m) = cnames
} else {
cnames = df[,2]
m = t(df[,-c(1:2)])
colnames(m) = cnames
}
return(data.frame(m))
})
setMethodS3("getClinicalData","CGDS", function(x, caseList='', cases=c(), caseIdsKey = '', ...) {
url = paste(x$.url, "webservice.do?cmd=getClinicalData",sep="")
if (length(cases)>0) { url = paste(url,"&case_list=", paste(cases,collapse=","),sep='')
} else if (caseIdsKey != '') { url = paste(url,"&case_ids_key=", caseIdsKey,sep='')
} else { url = paste(url,"&case_set_id=", caseList,sep='') }
df = processURL(x,url)
rownames(df) = make.names(df[,1])
return(df[,-1])
})
setMethodS3("plot","CGDS", function(x, cancerStudy, genes, geneticProfiles, caseList='', cases=c(), caseIdsKey = '', skin='cont', skin.normals='', skin.col.gp = c(), add.corr = '', legend.pos = 'topright', ...) {
errormsg <- function(msg,error=TRUE) {
# return empty plot with text
if (error) {msg = paste('Error:',msg)}
# override msg if global message provided in object
if (x$.ploterrormsg != '') {msg = x$.ploterrormsg}
plot.new()
# set message text here ...
#mtext(msg,cex=1.0,col='darkred')
text(0.5,0.5,msg,cex=1.0,col='darkred')
box()
return(msg)
}
# we only allow the following combinations
# a) gene1 (1 profile) # b) gene1 vs gene2 (1 profile)
# c) profile 1 vs profile 2 (1 gene)
if((length(genes) > 1 & length(geneticProfiles) > 1) | (length(genes) > 2 | length(geneticProfiles) > 2)) {
return(errormsg("use only 2 genetic profiles OR 2 genes"))
}
# make genenames conform to R variable names
genesR = make.names(genes)
# get data, check more than zero rows returned, otherwise return
df = getProfileData(x, genes, geneticProfiles, caseList, cases, caseIdsKey)
if (nrow(df) == 0) { return(errormsg(paste('empty data frame returned :\n',colnames(df)[1]))) }
# check data returned with more than two genes or genetic profiles
if (length(genes) == 2 & ncol(df) != 2) { return(errormsg(paste("gene not found:", setdiff(genesR,colnames(df))))) }
if (length(geneticProfiles) == 2 & ncol(df) != 2) { return(errormsg("geneticProfile ID not found:", setdiff(geneticProfiles,colnames(df)))) }
# get geneticProfiles annotation for axis labels
gps = getGeneticProfiles(x, cancerStudy)
if (nrow(gps) == 0) { errormsg(colnames(gps[1])) }
rownames(gps) = gps[,1]
gpaxisnames = gps[geneticProfiles,'genetic_profile_name']
names(gpaxisnames) = geneticProfiles
# we can have a situation where there is no data for a given combination of gene and genetic profile
# in this case, we have a column of NaN, and we generate an error
nacols = sapply(df, function(x) all(is.nan(x)))
if (any(nacols)) {
if (length(geneticProfiles) > 1) {
# two genetic profiles in columns, one gene
return(errormsg(paste(genes, "has no data\n for genetic profile(s):", paste(gpaxisnames[nacols],collapse=", ")),FALSE))
} else {
# one genetic profile, one or two genes in columns
return(errormsg(paste(paste(genes[nacols],collapse=' and '), "has no data\n for genetic profile:", gpaxisnames),FALSE))
}
}
# set sub title with correlation if specified
plot.subtitle = ''
if ((add.corr == 'pearson' | add.corr == 'spearman') & ncol(df) == 2) {
ct = cor.test(df[,1],df[,2],method=add.corr)
plot.subtitle = paste(add.corr, ' r = ', sprintf("%.2f",ct$estimate), ', p = ',sprintf("%.1e",ct$p.value))
}
###
### Skins
###
if (skin == 'cont') {
if(length(genes) == 1 & length(geneticProfiles) == 1) {
hist(df[,1],xlab=paste(genes," , ",gpaxisnames,sep=""),main='')
} else if (length(genes) == 2) {
# two genes
plot(df[,genesR[1]],df[,genesR[2]] , main = '', xlab = paste(genes[1],", ",gpaxisnames,sep=""), ylab = paste(genes[2],", ",gpaxisnames,sep=""), pch = 1, col = 'black', sub = plot.subtitle)
} else {
# two genetic profiles
gpa = geneticProfiles[1]
gpb = geneticProfiles[2]
plot(df[,gpa],df[,gpb] , main = '', xlab = paste(genes[1],", ",gpaxisnames[gpa],sep=""), ylab = paste(genes[1],", ",gpaxisnames[gpb],sep=""), pch = 1, col = 'black', sub = plot.subtitle)
}
} else if (skin == 'disc') {
if(length(genes) == 1 & length(geneticProfiles) == 1) {
barplot(table(df[,1]),xlab=paste(genes,", ",gpaxisnames,sep=""),main='',ylab='frequency')
} else {
#discrete vs discrete
return(errormsg('discrete vs. discrete data not implemented'))
}
} else if (skin =='disc_cont') {
# skin only valid for two genetic profiles
if(length(geneticProfiles) != 2) {
return(errormsg("two genetic profiles required for skin 'disc_cont'"))
} else {
# skin assumes that first genetic profile is discret
gp.disc = geneticProfiles[1] # b
gp.cont = geneticProfiles[2] # a
boxplot(df[,gp.cont] ~ df[,gp.disc], outpch = NA, main = '', xlab = paste(genes[1],", ",gpaxisnames[gp.disc],sep=""), ylab = paste(genes[1],", ",gpaxisnames[gp.cont],sep=""), border = 'gray', sub = plot.subtitle)
stripchart(df[,gp.cont] ~ df[,gp.disc],vertical = TRUE, add = TRUE, method = 'jitter', pch = 1, col = 'black')
}
} else if (skin == 'cna_mrna_mut') {
# skin uses parameters
# * skin.col.gp = mut
# * skin.normals = normal_case_set [optional]
# fetch optional normal mRNA data
if (skin.normals != '') {
df.norm = getProfileData(x, genes, geneticProfiles[2], skin.normals)
if (nrow(df.norm) == 0) { return(errormsg(paste('empty data frame returned :\n',colnames(df.norm)[1]))) }
# check if data is missing (NaN)
if ( !all(is.nan(df.norm[,1])) ) {
# add normal data to dataframe
df.norm2 = cbind(rep(-3,nrow(df.norm)),df.norm[,1])
colnames(df.norm2) = geneticProfiles
df = rbind(df,df.norm2)
}
}
# create boxplot
df.nona = df[apply(df, 1, function(x) {!any(is.na(x))}),]
ylim=range(df.nona[,geneticProfiles[2]],na.rm=TRUE)
labels=seq(-3,2)
names(labels)=c("Normal","Homdel","Hetloss","Diploid","Gain","Amp")
labels.inuse = sort(unique(df.nona[,geneticProfiles[1]])) # sort removes any NA
boxplot(df.nona[,geneticProfiles[2]] ~ df.nona[,geneticProfiles[1]], main='', outline=FALSE,
xlab = paste(genes,", ",gpaxisnames[geneticProfiles[1]],sep=""),
ylab = paste(genes,", ",gpaxisnames[geneticProfiles[2]],sep=""),
border="gray",ylim=ylim, axes=FALSE, outpch = NA, sub = plot.subtitle)
axis(1,at=seq(1,length(labels.inuse)),labels=names(labels)[match(labels.inuse,labels)],cex.axis=0.8)
axis(2,cex.axis=0.8,las=2)
# box()
# manually jitter data
# order data by CNA status
df.nona=df.nona[order(df.nona[,geneticProfiles[1]]),]
xy=list()
xy$MRNA=df.nona[,geneticProfiles[2]]
cats=cbind(1:length(labels.inuse),as.data.frame(table(df.nona[,geneticProfiles[1]])))
colnames(cats)=c("X","Class","Count")
rownames(cats)=names(labels)[match(cats[,2],labels)]
xy$JITTER = unlist( apply(cats,1, function(cc) {
y=rep.int(as.numeric(cc[1]),as.numeric(cc[3]))
y=y+stats::runif(length(y),-0.1,0.1)
}))
xy=as.data.frame(xy)
colnames(xy) = c('MRNA','JITTER')
# Initialize plotting features
nonmut.pch = 4
N=nrow(xy)
cex=rep(0.9,N)
pch=rep(nonmut.pch,N)
col=rep("royalblue",N)
bg=rep(NA,N)
# fetch mutation data for color coding
if (length(skin.col.gp == 1)) {
df.mut = getProfileData(x, genes, skin.col.gp, caseList, cases, caseIdsKey)
if (nrow(df.mut) == 0) { return(errormsg(paste('empty data frame returned :\n',colnames(df.mut)[1]))) }
# get matrix corresponding to df.nona
df.mut = df.mut[rownames(df.nona),1]
# check if data is missing (NaN)
mut=which(!is.na(df.mut))
if(length(mut)>0) {
# default mutation
col[mut]="red3"
bg[mut]="goldenrod"
pch[mut]=21
mt=list()
mt$pch=c(21,23,24,25,22)
mt$type=c("missense","nonsense","splice","shift","in_frame")
mt$pattern=c("^[a-z][0-9]+[a-z]$","[*x]$","^(e.+[0-9]|.+_splice)$","fs$","del$")
mt$bg=c("goldenrod","darkblue","darkgray","black","goldenrod")
mt=as.data.frame(mt)
for(i in 1:nrow(mt)) {
idx=grep(mt$pattern[i],tolower(df.mut))
pch[idx]=mt$pch[i]
bg[idx]=as.character(mt$bg[i])
}
#col[mut]="red3" # ??????
legend("topleft",bty="n",
as.character(as.vector(mt[["type"]])),col="red3",
pt.bg=as.character(as.vector(mt[["bg"]])),
pch=mt[["pch"]],cex=0.85,pt.cex=1.0
)
}
}
## # Plot the jittered data, add mutated points last
xy.mut = (pch != nonmut.pch)
points(xy$JITTER[!xy.mut],xy$MRNA[!xy.mut],pch=pch[!xy.mut],cex=cex[!xy.mut],col=col[!xy.mut],bg=bg[!xy.mut])
points(xy$JITTER[xy.mut],xy$MRNA[xy.mut],pch=pch[xy.mut],cex=cex[xy.mut],col=col[xy.mut],bg=bg[xy.mut])
box()
} else if (skin == 'meth_mrna_cna_mut' | skin == 'cna_mut') {
# these skins use parameters
# * skin.col.gp = (cna,mut) [optional]
# * skin.normals = normal_case_set [optional]
# [meth_mrna_cna_mut] forces x axis range to [0,1.05]
# fetch cna and mut data for color coding
pch=rep(1,nrow(df))
col=rep("black",nrow(df))
if (length(skin.col.gp) == 2) { # color by both CNA and mutation
df.col = getProfileData(x, genes, skin.col.gp, caseList, cases, caseIdsKey)
if (nrow(df.col) == 0) { return(errormsg(paste('empty data frame returned :\n',colnames(df.col)[1]))) }
# because mut is text vector, we need to transform cna to integer vector instead of factor
cna = as.integer(as.vector(df.col[,skin.col.gp[1]]))
mut = as.vector(df.col[,skin.col.gp[2]])
col[cna==-2]="darkblue"
col[cna==-1]="deepskyblue"
col[cna==1]="hotpink"
col[cna==2]="red3"
col[mut!="NaN"]="orange"
pch[mut!="NaN"]=20
}
else if (length(skin.col.gp) == 1) { # color only by CNA
df.col = getProfileData(x, genes, skin.col.gp, caseList, cases, caseIdsKey)
if (nrow(df.col) == 0) { return(errormsg(paste('empty data frame returned :\n',colnames(df.col)[1]))) }
# because mut is text vector, we need to transform cna to integer vector instead of factor
cna = as.integer(as.vector(df.col[,1]))
col[cna==-2]="darkblue"
col[cna==-1]="deepskyblue"
col[cna==1]="hotpink"
col[cna==2]="red3"
}
# fetch optional normal methylation and mRNA data
if (skin.normals != '') {
df.norm = getProfileData(x, genes, geneticProfiles, skin.normals)
if (nrow(df.norm) == 0) { return(errormsg(paste('empty data frame returned :\n',colnames(df.norm)[1]))) }
# remove missing data
df.norm = df.norm[apply(df.norm, 1, function(x) {!any(is.na(x))}),]
if ( length(df.norm) > 0) {
df = rbind(df,df.norm)
col = append(col, rep("black",nrow(df.norm)))
pch = append(pch, rep(20,nrow(df.norm)))
}
}
xlim = range(df[,geneticProfiles[1]],na.rm = TRUE)
# add 15% to range, to make room for legend
if (legend.pos == 'topright') {
xlim = c(min(xlim),max(xlim) + (max(xlim)-min(xlim))*0.15)
}
else if (legend.pos == 'topleft') {
xlim = c(min(xlim) - (max(xlim)-min(xlim))*0.15,max(xlim))
}
if (skin == 'meth_mrna_cna_mut') {
# force x axis range to [0,1.05]
xlim = c(0,1.05)
}
# now plot
plot( df[,geneticProfiles[1]],df[,geneticProfiles[2]],main="",
xlab=paste(genes,", ",gpaxisnames[geneticProfiles[1]],sep=""),
ylab=paste(genes,", ",gpaxisnames[geneticProfiles[2]],sep=""),
xlim=xlim,pch=pch,col=col,cex=1.2, sub = plot.subtitle
)
#abline(lm(d$rna~d$methylation),col="red3",lty=2,lwd=1.5)
#lines(loess.smooth(d$methylation,d$rna),col="darkgray",lwd=2)
# Replace with dynamically created legend when time permits
legend(legend.pos,bty="n",
c("Homdel","Hetloss","Diploid","Gain","Amp","Mutated","Normal"),
col=c('darkblue','deepskyblue','black','hotpink','red','orange','black'),
pch=c(1,1,1,1,1,20,20),cex=0.85,pt.cex=1.0
)
} else {
return(errormsg(paste("unkown skin:",skin)))
}
return(TRUE)
})
setMethodS3("test","CGDS", function(x, ...) {
checkEq = function(a,b) { if (identical(a,b)) "OK\n" else "FAILED!\n" }
checkGrt = function(a,b) { if (a > b) "OK\n" else "FAILED!\n" }
checkTrue = function(a) { if (a) "OK\n" else "FAILED!\n" }
cancerstudies = getCancerStudies(x)
cat('getCancerStudies... ',
checkEq(colnames(cancerstudies),c("cancer_study_id","name","description")))
ct = cancerstudies[2,1] # should be row 1 instead ...
cat('getCaseLists (1/2) ... ',
checkEq(colnames(getCaseLists(x,ct)),
c("case_list_id","case_list_name",
"case_list_description","cancer_study_id","case_ids")))
cat('getCaseLists (2/2) ... ',
checkEq(colnames(getCaseLists(x,'xxx')),
'Error..Problem.when.identifying.a.cancer.study.for.the.request.'))
cat('getGeneticProfiles (1/2) ... ',
checkEq(colnames(getGeneticProfiles(x,ct)),
c("genetic_profile_id","genetic_profile_name","genetic_profile_description",
"cancer_study_id","genetic_alteration_type","show_profile_in_analysis_tab")))
cat('getGeneticProfiles (2/2) ... ',
checkEq(colnames(getGeneticProfiles(x,'xxx')),
'Error..Problem.when.identifying.a.cancer.study.for.the.request.'))
# clinical data
# check colnames
cat('getClinicalData (1/1) ... ',
checkTrue("DFS_MONTHS" %in% colnames(getClinicalData(x,'gbm_tcga_all'))))
# check one gene, one profile
cat('getProfileData (1/6) ... ',
checkEq(colnames(getProfileData(x,'NF1','gbm_tcga_mrna','gbm_tcga_all')),
"NF1"))
# check many genes, one profile
cat('getProfileData (2/6) ... ',
checkEq(colnames(getProfileData(x,c('MDM2','MDM4'),'gbm_tcga_mrna','gbm_tcga_all')),
c("MDM2","MDM4")))
# check one gene, many profile
cat('getProfileData (3/6) ... ',
checkEq(colnames(getProfileData(x,'NF1',c('gbm_tcga_mrna','gbm_tcga_mutations'),'gbm_tcga_all')),
c('gbm_tcga_mrna','gbm_tcga_mutations')))
# check 3 cases returns matrix with 3 columns
cat('getProfileData (4/6) ... ',
checkEq(rownames(getProfileData(x,'BRCA1','gbm_tcga_mrna',cases=c('TCGA-02-0001-01','TCGA-02-0003-01'))),
make.names(c('TCGA-02-0001-01','TCGA-02-0003-01'))))
# invalid gene names return empty data.frame
cat('getProfileData (5/6) ... ',
checkEq(nrow(getProfileData(x,c('NF10','NF11'),'gbm_tcga_mrna','gbm_tcga_all')),as.integer(0)))
# invalid case_list_id returns error
cat('getProfileData (6/6) ... ',
checkEq(colnames(getProfileData(x,'NF1','gbm_tcga_mrna','xxx')),
'Error..Invalid.case_set_id...xxx.'))
})
cBioPortal/cgdsr documentation built on Dec. 15, 2020, 11:30 p.m.
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Defines functions .onAttach
library(R.oo)
.onAttach <- function(libname, pkgname){
packageStartupMessage('Please send questions to cbioportal@googlegroups.com')
}
setConstructorS3("CGDS", function(url='',verbose=FALSE,ploterrormsg='',token=NULL) {
extend(Object(), "CGDS",
.url=url,
.token=token,
.verbose=verbose,
.ploterrormsg='')
})
setMethodS3("processURL","CGDS", private=TRUE, function(x, url, force.comment.char.blank=FALSE, ...) {
if (x$.verbose) cat(url,"\n")
headers <- httr::add_headers()
if(!is.null(x$.token)) {
headers <- httr::add_headers(Authorization = paste("Bearer ", x$.token, sep = ""))
}
r <- httr::GET(url, headers)
httr::stop_for_status(r)
if(force.comment.char.blank) {
df = read.table(skip=0, header=TRUE, as.is=TRUE, sep="\t", quote='', comment.char='', fill=TRUE, text=httr::content(r, "text"))
} else {
df = read.table(skip=0, header=TRUE, as.is=TRUE, sep="\t", quote='', fill=TRUE, text=httr::content(r, "text"))
}
})
setMethodS3("setPlotErrorMsg","CGDS", function(x, msg, ...) {
x$.ploterrormsg = msg
return(msg)
})
setMethodS3("setVerbose","CGDS", function(x, verbose, ...) {
x$.verbose = verbose
return(verbose)
})
setMethodS3("getCancerStudies","CGDS", function(x, ...) {
url = paste(x$.url, "webservice.do?cmd=getCancerStudies&",sep="")
df = processURL(x,url)
return(df)
})
setMethodS3("getCaseLists","CGDS", function(x, cancerStudy, ...) {
url = paste(x$.url, "webservice.do?cmd=getCaseLists&cancer_study_id=", cancerStudy, sep="")
df = processURL(x,url)
return(df)
})
setMethodS3("getGeneticProfiles","CGDS", function(x, cancerStudy, ...) {
url = paste(x$.url, "webservice.do?cmd=getGeneticProfiles&cancer_study_id=", cancerStudy, sep="")
df = processURL(x,url)
return(df)
})
setMethodS3("getMutationData","CGDS", function(x, caseList, geneticProfile, genes, ...) {
url = paste(x$.url, "webservice.do?cmd=getMutationData",
"&case_set_id=", caseList,
"&genetic_profile_id=", geneticProfile,
"&gene_list=", paste(genes,collapse=","), sep="")
df = processURL(x,url)
return(df)
})
setMethodS3("getProfileData","CGDS", function(x, genes, geneticProfiles, caseList='', cases=c(), caseIdsKey = '', ...) {
url = paste(x$.url, "webservice.do?cmd=getProfileData",
"&gene_list=", paste(genes,collapse=","),
"&genetic_profile_id=", paste(geneticProfiles,collapse=","),
"&id_type=", 'gene_symbol',
sep="")
if (length(cases)>0) { url = paste(url,"&case_list=", paste(cases,collapse=","),sep='')
} else if (caseIdsKey != '') { url = paste(url,"&case_ids_key=", caseIdsKey,sep='')
} else { url = paste(url,"&case_set_id=", caseList,sep='') }
df = processURL(x,url)
if (nrow(df) == 0) { return(df) }
m = matrix()
# process data before returning
if (length(geneticProfiles) > 1) {
cnames = df[,1]
m = t(df[,-c(1:4)])
colnames(m) = cnames
} else {
cnames = df[,2]
m = t(df[,-c(1:2)])
colnames(m) = cnames
}
return(data.frame(m))
})
setMethodS3("getClinicalData","CGDS", function(x, caseList='', cases=c(), caseIdsKey = '', ...) {
url = paste(x$.url, "webservice.do?cmd=getClinicalData",sep="")
if (length(cases)>0) { url = paste(url,"&case_list=", paste(cases,collapse=","),sep='')
} else if (caseIdsKey != '') { url = paste(url,"&case_ids_key=", caseIdsKey,sep='')
} else { url = paste(url,"&case_set_id=", caseList,sep='') }
df = processURL(x,url)
rownames(df) = make.names(df[,1])
return(df[,-1])
})
setMethodS3("plot","CGDS", function(x, cancerStudy, genes, geneticProfiles, caseList='', cases=c(), caseIdsKey = '', skin='cont', skin.normals='', skin.col.gp = c(), add.corr = '', legend.pos = 'topright', ...) {
errormsg <- function(msg,error=TRUE) {
# return empty plot with text
if (error) {msg = paste('Error:',msg)}
# override msg if global message provided in object
if (x$.ploterrormsg != '') {msg = x$.ploterrormsg}
plot.new()
# set message text here ...
#mtext(msg,cex=1.0,col='darkred')
text(0.5,0.5,msg,cex=1.0,col='darkred')
box()
return(msg)
}
# we only allow the following combinations
# a) gene1 (1 profile) # b) gene1 vs gene2 (1 profile)
# c) profile 1 vs profile 2 (1 gene)
if((length(genes) > 1 & length(geneticProfiles) > 1) | (length(genes) > 2 | length(geneticProfiles) > 2)) {
return(errormsg("use only 2 genetic profiles OR 2 genes"))
}
# make genenames conform to R variable names
genesR = make.names(genes)
# get data, check more than zero rows returned, otherwise return
df = getProfileData(x, genes, geneticProfiles, caseList, cases, caseIdsKey)
if (nrow(df) == 0) { return(errormsg(paste('empty data frame returned :\n',colnames(df)[1]))) }
# check data returned with more than two genes or genetic profiles
if (length(genes) == 2 & ncol(df) != 2) { return(errormsg(paste("gene not found:", setdiff(genesR,colnames(df))))) }
if (length(geneticProfiles) == 2 & ncol(df) != 2) { return(errormsg("geneticProfile ID not found:", setdiff(geneticProfiles,colnames(df)))) }
# get geneticProfiles annotation for axis labels
gps = getGeneticProfiles(x, cancerStudy)
if (nrow(gps) == 0) { errormsg(colnames(gps[1])) }
rownames(gps) = gps[,1]
gpaxisnames = gps[geneticProfiles,'genetic_profile_name']
names(gpaxisnames) = geneticProfiles
# we can have a situation where there is no data for a given combination of gene and genetic profile
# in this case, we have a column of NaN, and we generate an error
nacols = sapply(df, function(x) all(is.nan(x)))
if (any(nacols)) {
if (length(geneticProfiles) > 1) {
# two genetic profiles in columns, one gene
return(errormsg(paste(genes, "has no data\n for genetic profile(s):", paste(gpaxisnames[nacols],collapse=", ")),FALSE))
} else {
# one genetic profile, one or two genes in columns
return(errormsg(paste(paste(genes[nacols],collapse=' and '), "has no data\n for genetic profile:", gpaxisnames),FALSE))
}
}
# set sub title with correlation if specified
plot.subtitle = ''
if ((add.corr == 'pearson' | add.corr == 'spearman') & ncol(df) == 2) {
ct = cor.test(df[,1],df[,2],method=add.corr)
plot.subtitle = paste(add.corr, ' r = ', sprintf("%.2f",ct$estimate), ', p = ',sprintf("%.1e",ct$p.value))
}
###
### Skins
###
if (skin == 'cont') {
if(length(genes) == 1 & length(geneticProfiles) == 1) {
hist(df[,1],xlab=paste(genes," , ",gpaxisnames,sep=""),main='')
} else if (length(genes) == 2) {
# two genes
plot(df[,genesR[1]],df[,genesR[2]] , main = '', xlab = paste(genes[1],", ",gpaxisnames,sep=""), ylab = paste(genes[2],", ",gpaxisnames,sep=""), pch = 1, col = 'black', sub = plot.subtitle)
} else {
# two genetic profiles
gpa = geneticProfiles[1]
gpb = geneticProfiles[2]
plot(df[,gpa],df[,gpb] , main = '', xlab = paste(genes[1],", ",gpaxisnames[gpa],sep=""), ylab = paste(genes[1],", ",gpaxisnames[gpb],sep=""), pch = 1, col = 'black', sub = plot.subtitle)
}
} else if (skin == 'disc') {
if(length(genes) == 1 & length(geneticProfiles) == 1) {
barplot(table(df[,1]),xlab=paste(genes,", ",gpaxisnames,sep=""),main='',ylab='frequency')
} else {
#discrete vs discrete
return(errormsg('discrete vs. discrete data not implemented'))
}
} else if (skin =='disc_cont') {
# skin only valid for two genetic profiles
if(length(geneticProfiles) != 2) {
return(errormsg("two genetic profiles required for skin 'disc_cont'"))
} else {
# skin assumes that first genetic profile is discret
gp.disc = geneticProfiles[1] # b
gp.cont = geneticProfiles[2] # a
boxplot(df[,gp.cont] ~ df[,gp.disc], outpch = NA, main = '', xlab = paste(genes[1],", ",gpaxisnames[gp.disc],sep=""), ylab = paste(genes[1],", ",gpaxisnames[gp.cont],sep=""), border = 'gray', sub = plot.subtitle)
stripchart(df[,gp.cont] ~ df[,gp.disc],vertical = TRUE, add = TRUE, method = 'jitter', pch = 1, col = 'black')
}
} else if (skin == 'cna_mrna_mut') {
# skin uses parameters
# * skin.col.gp = mut
# * skin.normals = normal_case_set [optional]
# fetch optional normal mRNA data
if (skin.normals != '') {
df.norm = getProfileData(x, genes, geneticProfiles[2], skin.normals)
if (nrow(df.norm) == 0) { return(errormsg(paste('empty data frame returned :\n',colnames(df.norm)[1]))) }
# check if data is missing (NaN)
if ( !all(is.nan(df.norm[,1])) ) {
# add normal data to dataframe
df.norm2 = cbind(rep(-3,nrow(df.norm)),df.norm[,1])
colnames(df.norm2) = geneticProfiles
df = rbind(df,df.norm2)
}
}
# create boxplot
df.nona = df[apply(df, 1, function(x) {!any(is.na(x))}),]
ylim=range(df.nona[,geneticProfiles[2]],na.rm=TRUE)
labels=seq(-3,2)
names(labels)=c("Normal","Homdel","Hetloss","Diploid","Gain","Amp")
labels.inuse = sort(unique(df.nona[,geneticProfiles[1]])) # sort removes any NA
boxplot(df.nona[,geneticProfiles[2]] ~ df.nona[,geneticProfiles[1]], main='', outline=FALSE,
xlab = paste(genes,", ",gpaxisnames[geneticProfiles[1]],sep=""),
ylab = paste(genes,", ",gpaxisnames[geneticProfiles[2]],sep=""),
border="gray",ylim=ylim, axes=FALSE, outpch = NA, sub = plot.subtitle)
axis(1,at=seq(1,length(labels.inuse)),labels=names(labels)[match(labels.inuse,labels)],cex.axis=0.8)
axis(2,cex.axis=0.8,las=2)
# box()
# manually jitter data
# order data by CNA status
df.nona=df.nona[order(df.nona[,geneticProfiles[1]]),]
xy=list()
xy$MRNA=df.nona[,geneticProfiles[2]]
cats=cbind(1:length(labels.inuse),as.data.frame(table(df.nona[,geneticProfiles[1]])))
colnames(cats)=c("X","Class","Count")
rownames(cats)=names(labels)[match(cats[,2],labels)]
xy$JITTER = unlist( apply(cats,1, function(cc) {
y=rep.int(as.numeric(cc[1]),as.numeric(cc[3]))
y=y+stats::runif(length(y),-0.1,0.1)
}))
xy=as.data.frame(xy)
colnames(xy) = c('MRNA','JITTER')
# Initialize plotting features
nonmut.pch = 4
N=nrow(xy)
cex=rep(0.9,N)
pch=rep(nonmut.pch,N)
col=rep("royalblue",N)
bg=rep(NA,N)
# fetch mutation data for color coding
if (length(skin.col.gp == 1)) {
df.mut = getProfileData(x, genes, skin.col.gp, caseList, cases, caseIdsKey)
if (nrow(df.mut) == 0) { return(errormsg(paste('empty data frame returned :\n',colnames(df.mut)[1]))) }
# get matrix corresponding to df.nona
df.mut = df.mut[rownames(df.nona),1]
# check if data is missing (NaN)
mut=which(!is.na(df.mut))
if(length(mut)>0) {
# default mutation
col[mut]="red3"
bg[mut]="goldenrod"
pch[mut]=21
mt=list()
mt$pch=c(21,23,24,25,22)
mt$type=c("missense","nonsense","splice","shift","in_frame")
mt$pattern=c("^[a-z][0-9]+[a-z]$","[*x]$","^(e.+[0-9]|.+_splice)$","fs$","del$")
mt$bg=c("goldenrod","darkblue","darkgray","black","goldenrod")
mt=as.data.frame(mt)
for(i in 1:nrow(mt)) {
idx=grep(mt$pattern[i],tolower(df.mut))
pch[idx]=mt$pch[i]
bg[idx]=as.character(mt$bg[i])
}
#col[mut]="red3" # ??????
legend("topleft",bty="n",
as.character(as.vector(mt[["type"]])),col="red3",
pt.bg=as.character(as.vector(mt[["bg"]])),
pch=mt[["pch"]],cex=0.85,pt.cex=1.0
)
}
}
## # Plot the jittered data, add mutated points last
xy.mut = (pch != nonmut.pch)
points(xy$JITTER[!xy.mut],xy$MRNA[!xy.mut],pch=pch[!xy.mut],cex=cex[!xy.mut],col=col[!xy.mut],bg=bg[!xy.mut])
points(xy$JITTER[xy.mut],xy$MRNA[xy.mut],pch=pch[xy.mut],cex=cex[xy.mut],col=col[xy.mut],bg=bg[xy.mut])
box()
} else if (skin == 'meth_mrna_cna_mut' | skin == 'cna_mut') {
# these skins use parameters
# * skin.col.gp = (cna,mut) [optional]
# * skin.normals = normal_case_set [optional]
# [meth_mrna_cna_mut] forces x axis range to [0,1.05]
# fetch cna and mut data for color coding
pch=rep(1,nrow(df))
col=rep("black",nrow(df))
if (length(skin.col.gp) == 2) { # color by both CNA and mutation
df.col = getProfileData(x, genes, skin.col.gp, caseList, cases, caseIdsKey)
if (nrow(df.col) == 0) { return(errormsg(paste('empty data frame returned :\n',colnames(df.col)[1]))) }
# because mut is text vector, we need to transform cna to integer vector instead of factor
cna = as.integer(as.vector(df.col[,skin.col.gp[1]]))
mut = as.vector(df.col[,skin.col.gp[2]])
col[cna==-2]="darkblue"
col[cna==-1]="deepskyblue"
col[cna==1]="hotpink"
col[cna==2]="red3"
col[mut!="NaN"]="orange"
pch[mut!="NaN"]=20
}
else if (length(skin.col.gp) == 1) { # color only by CNA
df.col = getProfileData(x, genes, skin.col.gp, caseList, cases, caseIdsKey)
if (nrow(df.col) == 0) { return(errormsg(paste('empty data frame returned :\n',colnames(df.col)[1]))) }
# because mut is text vector, we need to transform cna to integer vector instead of factor
cna = as.integer(as.vector(df.col[,1]))
col[cna==-2]="darkblue"
col[cna==-1]="deepskyblue"
col[cna==1]="hotpink"
col[cna==2]="red3"
}
# fetch optional normal methylation and mRNA data
if (skin.normals != '') {
df.norm = getProfileData(x, genes, geneticProfiles, skin.normals)
if (nrow(df.norm) == 0) { return(errormsg(paste('empty data frame returned :\n',colnames(df.norm)[1]))) }
# remove missing data
df.norm = df.norm[apply(df.norm, 1, function(x) {!any(is.na(x))}),]
if ( length(df.norm) > 0) {
df = rbind(df,df.norm)
col = append(col, rep("black",nrow(df.norm)))
pch = append(pch, rep(20,nrow(df.norm)))
}
}
xlim = range(df[,geneticProfiles[1]],na.rm = TRUE)
# add 15% to range, to make room for legend
if (legend.pos == 'topright') {
xlim = c(min(xlim),max(xlim) + (max(xlim)-min(xlim))*0.15)
}
else if (legend.pos == 'topleft') {
xlim = c(min(xlim) - (max(xlim)-min(xlim))*0.15,max(xlim))
}
if (skin == 'meth_mrna_cna_mut') {
# force x axis range to [0,1.05]
xlim = c(0,1.05)
}
# now plot
plot( df[,geneticProfiles[1]],df[,geneticProfiles[2]],main="",
xlab=paste(genes,", ",gpaxisnames[geneticProfiles[1]],sep=""),
ylab=paste(genes,", ",gpaxisnames[geneticProfiles[2]],sep=""),
xlim=xlim,pch=pch,col=col,cex=1.2, sub = plot.subtitle
)
#abline(lm(d$rna~d$methylation),col="red3",lty=2,lwd=1.5)
#lines(loess.smooth(d$methylation,d$rna),col="darkgray",lwd=2)
# Replace with dynamically created legend when time permits
legend(legend.pos,bty="n",
c("Homdel","Hetloss","Diploid","Gain","Amp","Mutated","Normal"),
col=c('darkblue','deepskyblue','black','hotpink','red','orange','black'),
pch=c(1,1,1,1,1,20,20),cex=0.85,pt.cex=1.0
)
} else {
return(errormsg(paste("unkown skin:",skin)))
}
return(TRUE)
})
setMethodS3("test","CGDS", function(x, ...) {
checkEq = function(a,b) { if (identical(a,b)) "OK\n" else "FAILED!\n" }
checkGrt = function(a,b) { if (a > b) "OK\n" else "FAILED!\n" }
checkTrue = function(a) { if (a) "OK\n" else "FAILED!\n" }
cancerstudies = getCancerStudies(x)
cat('getCancerStudies... ',
checkEq(colnames(cancerstudies),c("cancer_study_id","name","description")))
ct = cancerstudies[2,1] # should be row 1 instead ...
cat('getCaseLists (1/2) ... ',
checkEq(colnames(getCaseLists(x,ct)),
c("case_list_id","case_list_name",
"case_list_description","cancer_study_id","case_ids")))
cat('getCaseLists (2/2) ... ',
checkEq(colnames(getCaseLists(x,'xxx')),
'Error..Problem.when.identifying.a.cancer.study.for.the.request.'))
cat('getGeneticProfiles (1/2) ... ',
checkEq(colnames(getGeneticProfiles(x,ct)),
c("genetic_profile_id","genetic_profile_name","genetic_profile_description",
"cancer_study_id","genetic_alteration_type","show_profile_in_analysis_tab")))
cat('getGeneticProfiles (2/2) ... ',
checkEq(colnames(getGeneticProfiles(x,'xxx')),
'Error..Problem.when.identifying.a.cancer.study.for.the.request.'))
# clinical data
# check colnames
cat('getClinicalData (1/1) ... ',
checkTrue("DFS_MONTHS" %in% colnames(getClinicalData(x,'gbm_tcga_all'))))
# check one gene, one profile
cat('getProfileData (1/6) ... ',
checkEq(colnames(getProfileData(x,'NF1','gbm_tcga_mrna','gbm_tcga_all')),
"NF1"))
# check many genes, one profile
cat('getProfileData (2/6) ... ',
checkEq(colnames(getProfileData(x,c('MDM2','MDM4'),'gbm_tcga_mrna','gbm_tcga_all')),
c("MDM2","MDM4")))
# check one gene, many profile
cat('getProfileData (3/6) ... ',
checkEq(colnames(getProfileData(x,'NF1',c('gbm_tcga_mrna','gbm_tcga_mutations'),'gbm_tcga_all')),
c('gbm_tcga_mrna','gbm_tcga_mutations')))
# check 3 cases returns matrix with 3 columns
cat('getProfileData (4/6) ... ',
checkEq(rownames(getProfileData(x,'BRCA1','gbm_tcga_mrna',cases=c('TCGA-02-0001-01','TCGA-02-0003-01'))),
make.names(c('TCGA-02-0001-01','TCGA-02-0003-01'))))
# invalid gene names return empty data.frame
cat('getProfileData (5/6) ... ',
checkEq(nrow(getProfileData(x,c('NF10','NF11'),'gbm_tcga_mrna','gbm_tcga_all')),as.integer(0)))
# invalid case_list_id returns error
cat('getProfileData (6/6) ... ',
checkEq(colnames(getProfileData(x,'NF1','gbm_tcga_mrna','xxx')),
'Error..Invalid.case_set_id...xxx.'))
})
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