R/outputReport.R
In GaoLabXDU/CEPICS: CEPICS: a comparison and evaluation platform for integration methods in cancer subtyping
Defines functions
outputReport
#' @export
outputReport <- function(method=list('SNF','LRA','iCluster','PINS'),pic_eval=list('HeatMap','KM'),pinsk=c(2,3),numeric_eval=list('NMI','ARI','SI'),
need_gold_eval=list('NMI','ARI'),is_gold=TRUE,n_pic_row=2,kmax=7,path='',
filename='report.Rmd',title='Evaluation and Comparison Report',author="",is_report=TRUE,num_truelabel=0) {
eval_full_name=list("NMI"="Normalized Mutual Information","ARI"="Adjusted Rand Index","SI"="Silhouette Coefficient","RI"="Rand Index","KM"="Kaplan-Meier Survival Curves","P-value"="-Log10(Cox P-value)","SC"="Silhouette Coefficient")
method_full_name=list("PFA"="PFA","iCluster"="iClusterBayes","LRA"="LRAcluster","PINS"="PINS","SNF"="SNF")
pf=paste(path,filename,sep='/')
has_PINS=FALSE
newmethod=list()
for(e in method)
if(e!="PINS")
newmethod=append(newmethod,e)
else
has_PINS=TRUE
method=newmethod
writeHeader(header = list(title=title,author=author,
date=paste(strsplit(as.character(Sys.time()),split=' ')[[1]][1],
strsplit(as.character(Sys.time()),split=' ')[[1]][2])),filename = pf)
if(!is_report)
writeCode('',list(echo=FALSE,inlcude=FALSE,warning = FALSE,message = FALSE,error = FALSE),code='knitr::opts_chunk$set(dev="pdf",fig.path="fig/")' ,filename = pf)
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code='
options(warn =-1)
library(pheatmap)
library(survival)
library(ggplot2)
library(grid)
library(reshape2)
library(ggthemr)
ggthemr("fresh")
' ,filename = pf)
h('Time Consumption',1,pf)
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code='load("timeList.RData")\ndrawtime(timeList)' ,filename = pf)
writeRmd('\n\n',pf)
concat <- function(xx,sep='',n=1) {
s=""
for(e in xx)
{
s=paste(s,e,sep=sep)
}
return(substr(s,n,nchar(s)))
}
if(is_gold)
{
h('Comparison based on True Labels',1,pf)
h(paste('There are',num_truelabel,'clusters in true label'),3,pf)
lst=list(c(1,1),c(1,2),c(2,1),c(2,2))
xxx=1
code="pushViewport(viewport(layout = grid.layout(2,2)))"
for (e in list("P-value","NMI","ARI","SC")) {
fnm=paste(path,"/goldMatrix_",e,".RData",sep="")
if(file.exists(fnm))
{
fnm1=paste("goldMatrix_",e,sep="")
code=paste(code,'\ndrawBarRmd("', fnm1 ,'",ylabel="',eval_full_name[[e]],'",vp=c(',lst[[xxx]][1] ,',' ,lst[[xxx]][2] ,'))' ,sep="")
}
xxx=xxx+1
}
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code=code ,filename = pf)
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code="
drawzmat('Metrices','Methods',key='Score')
" ,filename = pf)
}
if(length(method)!=0 && "KM" %in% pic_eval)
{
h('Survival Analysis',1,pf)
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code=paste('drawPvalues(method=list(',concat(method,sep='","',n=3),'"),k=c(',2,':',kmax,'))',sep='') ,filename = pf)
}
if(length(method)!=0)
{
if(is_gold)
{
for(e in numeric_eval)
{
if(e %in% need_gold_eval )
{
h(eval_full_name[[e]],1,pf)
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code=paste('drawBarRmd("',e,'",',kmax,',"',eval_full_name[e],'")',sep='') ,filename = pf)
}
}
for(e in numeric_eval)
{
if(!(e %in% need_gold_eval) )
{
h(eval_full_name[[e]],1,pf)
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code=paste('drawBarRmd("',e,'",',kmax,',"',eval_full_name[e],'")',sep='') ,filename = pf)
}
}
}
else
{
h(paste(eval_full_name[['NMI']],"and",eval_full_name[['ARI']]) ,1,pf)
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code=paste('
load("meanNMI.RData")
load("meanARI.RData")
drawHeatmapRmd(list(meanNMI,meanARI),title=list("NMI","ARI"),xlabel="Methods",ylabel="Number of Clusters")',sep='') ,filename = pf)
for(i in (2:kmax))
{
h(paste('Comparison Based on',i,'Clusters') ,2,pf)
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code=paste('load("nogold_method.RData")
drawHeatmapRmd(list(nogold_method[["NMI"]][["',i,'"]],nogold_method[["ARI"]][["',i,'"]]),title=list("NMI","ARI"))',sep='') ,filename = pf)
}
if('SI' %in% numeric_eval)
{
h(eval_full_name[['SI']],1,pf)
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code=paste('drawBarRmd("','SI','",',kmax,',"',eval_full_name["SI"],'")',sep='') ,filename = pf)
}
}
h('Samples Similarity HeatMap',1,pf)
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code=paste('
load("sampleClu.RData")
sampleClusterFig(sampleClu)',sep='') ,filename = pf)
}
writeRmd('========================================================================================',filename = pf)
writeRmd('========================================================================================',filename = pf)
h('Performance of Each Method',1,pf)
for(e in method)
{
s=""
if(is.null(method_full_name[[e]]))
s=e
else
s=method_full_name[[e]]
h(s,2,pf)
if(is_gold)
{
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code=paste('table=drawtable_all_eval("',e,'",list(',
concat(numeric_eval,'","',n=3),'"),list(',concat(pic_eval,'","',n=3),'"),c(',2,':',kmax,')',')' ,sep='') ,filename = pf)
h('Results of Different Metrics',3,filename = pf)
ss=""
i=0
for(ee in numeric_eval)
{
if(ee=='SI')
aa=paste("SC","-----",eval_full_name[[ee]])
else
aa=paste(ee,"-----",eval_full_name[[ee]])
for(nbb in c(nchar(aa):45))
aa=paste(aa," ",sep="")
ss=paste(ss,aa)
if(i%%2==1)
{
writeRmd(ss,filename=pf)
writeRmd("\n",filename=pf)
ss=""
}
i=i+1
}
if(length(numeric_eval)%%2==1)
{
writeRmd(ss,filename=pf)
writeRmd("\n",filename=pf)
}
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code=paste('
drawHeatmapRmd(list(t(table)),manyeval=TRUE,x_continuous=TRUE,k=as.integer(colnames(table)),x="Number of Clusters")',sep='') ,filename = pf)
}
if('KM' %in% pic_eval)
{
h('Kaplan-Meier Survival Curves
',3,pf)
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code=paste('\n') ,closechunk = FALSE,filename = pf)
writeRmd(paste('par(mfrow=c(1,',n_pic_row,'))\n'),filename = pf)
i=1
for (c in c(2:kmax))
{
if(c!=2 && c%%n_pic_row==0)
{
writeRmd(paste('```\n'),filename = pf)
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code=paste('\n') ,closechunk = FALSE,filename = pf)
i=i+1
writeRmd(paste('par(mfrow=c(1,',n_pic_row,'))\n'),filename = pf)
}
writeRmd(paste('load("F_',e,'_',c,'_KM.RData")\n',sep='') ,filename = pf)
writeRmd(paste('drawKMcurve(kmData,"Number of Clusters: ', c ,'")\n') ,filename = pf)
}
writeRmd(paste('```\n'),filename = pf)
}
if('HeatMap' %in% pic_eval)
{
h('HeatMaps',3,pf)
for (c in c(2:kmax))
{
h(paste('Number of Clusters: ',c,sep=""),4,pf)
writeCode('',list(echo=FALSE,inlcude=TRUE,fig.width=5.8,warning = FALSE,message = FALSE,error = FALSE),code=paste('\n'),closechunk = FALSE,filename = pf)
writeRmd(paste('load("F_',e,'_',c,'_heatmap.RData")\n',sep='') ,filename = pf)
writeRmd('pheatmap(hmData$jz,cluster_rows = FALSE, cluster_cols = FALSE,color = colorRampPalette(c("#294998", "#0672ba", "#0ba9de", "#48c4ed", "#9ad8f0", "#ffffff", "#f7d6ad", "#f9ae82", "#ef837b", "#dc515a", "#ae3c4a"))(50), show_rownames = FALSE, show_colnames = FALSE)\n',filename = pf)
writeRmd(paste('```\n'),filename = pf)
}
}
}
if(has_PINS)
{
if(!(!("KM" %in% pic_eval) && !is_gold))
h('PINS',2,pf)
if(is_gold)
{
e="PINS"
if(length(pinsk)>1)
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code=paste('table=drawtable_all_eval("',e,'",list(',
concat(numeric_eval,'","',n=3),'"),list(',concat(pic_eval,'","',n=3),'"),c(',pinsk[1],',',pinsk[2],')',')' ,sep='') ,filename = pf)
else
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code=paste('table=drawtable_all_eval("',e,'",list(',
concat(numeric_eval,'","',n=3),'"),list(',concat(pic_eval,'","',n=3),'"),c(',pinsk[1],')',')' ,sep='') ,filename = pf)
h('Results of Different Metrics',3,filename = pf)
ss=""
i=0
for(ee in numeric_eval)
{
if(ee=='SI')
aa=paste("SC","-----",eval_full_name[[ee]])
else
aa=paste(ee,"-----",eval_full_name[[ee]])
for(nbb in c(nchar(aa):45))
aa=paste(aa," ",sep="")
ss=paste(ss,aa)
if(i%%2==1)
{
writeRmd(ss,filename=pf)
writeRmd("\n",filename=pf)
ss=""
}
i=i+1
}
if(length(numeric_eval)%%2==1)
{
writeRmd(ss,filename=pf)
writeRmd("\n",filename=pf)
}
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code=paste('
drawHeatmapRmd(list(t(table)),manyeval=TRUE,x_continuous=TRUE,k=as.integer(colnames(table)),x="Number of Clusters")',sep='') ,filename = pf)
}
if("KM"%in% pic_eval)
{
h('Kaplan-Meier Survival Curves',3,pf)
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code=paste('\n'),closechunk = FALSE,filename = pf)
writeRmd(paste('par(mfrow=c(1,',n_pic_row,'))\n'),filename = pf)
s=paste("F_PINS_",pinsk[[1]],"_KM.RData",sep='')
writeRmd(paste('load("',s,'")\n',sep='') ,filename = pf)
writeRmd(paste('drawKMcurve(kmData,"Number of Clusters: ', pinsk[[1]] ,'")\n') ,filename = pf)
if(length(pinsk)>1)
{
s=paste("F_PINS_",pinsk[[2]],"_KM.RData",sep='')
writeRmd(paste('load("',s,'")\n',sep='') ,filename = pf)
writeRmd(paste('drawKMcurve(kmData,"Number of Clusters: ', pinsk[[2]] ,'")\n') ,filename = pf)
}
writeRmd(paste('```\n'),filename = pf)
}
}
render(pf, html_document())
if(is_report)
delfile(pf)
else
{
delfile(pf)
pf=paste(path,'/',strsplit(filename,".",fixed =TRUE)[[1]][1],".html",sep='')
delfile(pf)
}
}
GaoLabXDU/CEPICS documentation built on June 9, 2020, 2:31 a.m.
R Package Documentation
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Defines functions outputReport
#' @export
outputReport <- function(method=list('SNF','LRA','iCluster','PINS'),pic_eval=list('HeatMap','KM'),pinsk=c(2,3),numeric_eval=list('NMI','ARI','SI'),
need_gold_eval=list('NMI','ARI'),is_gold=TRUE,n_pic_row=2,kmax=7,path='',
filename='report.Rmd',title='Evaluation and Comparison Report',author="",is_report=TRUE,num_truelabel=0) {
eval_full_name=list("NMI"="Normalized Mutual Information","ARI"="Adjusted Rand Index","SI"="Silhouette Coefficient","RI"="Rand Index","KM"="Kaplan-Meier Survival Curves","P-value"="-Log10(Cox P-value)","SC"="Silhouette Coefficient")
method_full_name=list("PFA"="PFA","iCluster"="iClusterBayes","LRA"="LRAcluster","PINS"="PINS","SNF"="SNF")
pf=paste(path,filename,sep='/')
has_PINS=FALSE
newmethod=list()
for(e in method)
if(e!="PINS")
newmethod=append(newmethod,e)
else
has_PINS=TRUE
method=newmethod
writeHeader(header = list(title=title,author=author,
date=paste(strsplit(as.character(Sys.time()),split=' ')[[1]][1],
strsplit(as.character(Sys.time()),split=' ')[[1]][2])),filename = pf)
if(!is_report)
writeCode('',list(echo=FALSE,inlcude=FALSE,warning = FALSE,message = FALSE,error = FALSE),code='knitr::opts_chunk$set(dev="pdf",fig.path="fig/")' ,filename = pf)
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code='
options(warn =-1)
library(pheatmap)
library(survival)
library(ggplot2)
library(grid)
library(reshape2)
library(ggthemr)
ggthemr("fresh")
' ,filename = pf)
h('Time Consumption',1,pf)
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code='load("timeList.RData")\ndrawtime(timeList)' ,filename = pf)
writeRmd('\n\n',pf)
concat <- function(xx,sep='',n=1) {
s=""
for(e in xx)
{
s=paste(s,e,sep=sep)
}
return(substr(s,n,nchar(s)))
}
if(is_gold)
{
h('Comparison based on True Labels',1,pf)
h(paste('There are',num_truelabel,'clusters in true label'),3,pf)
lst=list(c(1,1),c(1,2),c(2,1),c(2,2))
xxx=1
code="pushViewport(viewport(layout = grid.layout(2,2)))"
for (e in list("P-value","NMI","ARI","SC")) {
fnm=paste(path,"/goldMatrix_",e,".RData",sep="")
if(file.exists(fnm))
{
fnm1=paste("goldMatrix_",e,sep="")
code=paste(code,'\ndrawBarRmd("', fnm1 ,'",ylabel="',eval_full_name[[e]],'",vp=c(',lst[[xxx]][1] ,',' ,lst[[xxx]][2] ,'))' ,sep="")
}
xxx=xxx+1
}
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code=code ,filename = pf)
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code="
drawzmat('Metrices','Methods',key='Score')
" ,filename = pf)
}
if(length(method)!=0 && "KM" %in% pic_eval)
{
h('Survival Analysis',1,pf)
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code=paste('drawPvalues(method=list(',concat(method,sep='","',n=3),'"),k=c(',2,':',kmax,'))',sep='') ,filename = pf)
}
if(length(method)!=0)
{
if(is_gold)
{
for(e in numeric_eval)
{
if(e %in% need_gold_eval )
{
h(eval_full_name[[e]],1,pf)
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code=paste('drawBarRmd("',e,'",',kmax,',"',eval_full_name[e],'")',sep='') ,filename = pf)
}
}
for(e in numeric_eval)
{
if(!(e %in% need_gold_eval) )
{
h(eval_full_name[[e]],1,pf)
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code=paste('drawBarRmd("',e,'",',kmax,',"',eval_full_name[e],'")',sep='') ,filename = pf)
}
}
}
else
{
h(paste(eval_full_name[['NMI']],"and",eval_full_name[['ARI']]) ,1,pf)
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code=paste('
load("meanNMI.RData")
load("meanARI.RData")
drawHeatmapRmd(list(meanNMI,meanARI),title=list("NMI","ARI"),xlabel="Methods",ylabel="Number of Clusters")',sep='') ,filename = pf)
for(i in (2:kmax))
{
h(paste('Comparison Based on',i,'Clusters') ,2,pf)
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code=paste('load("nogold_method.RData")
drawHeatmapRmd(list(nogold_method[["NMI"]][["',i,'"]],nogold_method[["ARI"]][["',i,'"]]),title=list("NMI","ARI"))',sep='') ,filename = pf)
}
if('SI' %in% numeric_eval)
{
h(eval_full_name[['SI']],1,pf)
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code=paste('drawBarRmd("','SI','",',kmax,',"',eval_full_name["SI"],'")',sep='') ,filename = pf)
}
}
h('Samples Similarity HeatMap',1,pf)
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code=paste('
load("sampleClu.RData")
sampleClusterFig(sampleClu)',sep='') ,filename = pf)
}
writeRmd('========================================================================================',filename = pf)
writeRmd('========================================================================================',filename = pf)
h('Performance of Each Method',1,pf)
for(e in method)
{
s=""
if(is.null(method_full_name[[e]]))
s=e
else
s=method_full_name[[e]]
h(s,2,pf)
if(is_gold)
{
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code=paste('table=drawtable_all_eval("',e,'",list(',
concat(numeric_eval,'","',n=3),'"),list(',concat(pic_eval,'","',n=3),'"),c(',2,':',kmax,')',')' ,sep='') ,filename = pf)
h('Results of Different Metrics',3,filename = pf)
ss=""
i=0
for(ee in numeric_eval)
{
if(ee=='SI')
aa=paste("SC","-----",eval_full_name[[ee]])
else
aa=paste(ee,"-----",eval_full_name[[ee]])
for(nbb in c(nchar(aa):45))
aa=paste(aa," ",sep="")
ss=paste(ss,aa)
if(i%%2==1)
{
writeRmd(ss,filename=pf)
writeRmd("\n",filename=pf)
ss=""
}
i=i+1
}
if(length(numeric_eval)%%2==1)
{
writeRmd(ss,filename=pf)
writeRmd("\n",filename=pf)
}
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code=paste('
drawHeatmapRmd(list(t(table)),manyeval=TRUE,x_continuous=TRUE,k=as.integer(colnames(table)),x="Number of Clusters")',sep='') ,filename = pf)
}
if('KM' %in% pic_eval)
{
h('Kaplan-Meier Survival Curves
',3,pf)
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code=paste('\n') ,closechunk = FALSE,filename = pf)
writeRmd(paste('par(mfrow=c(1,',n_pic_row,'))\n'),filename = pf)
i=1
for (c in c(2:kmax))
{
if(c!=2 && c%%n_pic_row==0)
{
writeRmd(paste('```\n'),filename = pf)
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code=paste('\n') ,closechunk = FALSE,filename = pf)
i=i+1
writeRmd(paste('par(mfrow=c(1,',n_pic_row,'))\n'),filename = pf)
}
writeRmd(paste('load("F_',e,'_',c,'_KM.RData")\n',sep='') ,filename = pf)
writeRmd(paste('drawKMcurve(kmData,"Number of Clusters: ', c ,'")\n') ,filename = pf)
}
writeRmd(paste('```\n'),filename = pf)
}
if('HeatMap' %in% pic_eval)
{
h('HeatMaps',3,pf)
for (c in c(2:kmax))
{
h(paste('Number of Clusters: ',c,sep=""),4,pf)
writeCode('',list(echo=FALSE,inlcude=TRUE,fig.width=5.8,warning = FALSE,message = FALSE,error = FALSE),code=paste('\n'),closechunk = FALSE,filename = pf)
writeRmd(paste('load("F_',e,'_',c,'_heatmap.RData")\n',sep='') ,filename = pf)
writeRmd('pheatmap(hmData$jz,cluster_rows = FALSE, cluster_cols = FALSE,color = colorRampPalette(c("#294998", "#0672ba", "#0ba9de", "#48c4ed", "#9ad8f0", "#ffffff", "#f7d6ad", "#f9ae82", "#ef837b", "#dc515a", "#ae3c4a"))(50), show_rownames = FALSE, show_colnames = FALSE)\n',filename = pf)
writeRmd(paste('```\n'),filename = pf)
}
}
}
if(has_PINS)
{
if(!(!("KM" %in% pic_eval) && !is_gold))
h('PINS',2,pf)
if(is_gold)
{
e="PINS"
if(length(pinsk)>1)
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code=paste('table=drawtable_all_eval("',e,'",list(',
concat(numeric_eval,'","',n=3),'"),list(',concat(pic_eval,'","',n=3),'"),c(',pinsk[1],',',pinsk[2],')',')' ,sep='') ,filename = pf)
else
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code=paste('table=drawtable_all_eval("',e,'",list(',
concat(numeric_eval,'","',n=3),'"),list(',concat(pic_eval,'","',n=3),'"),c(',pinsk[1],')',')' ,sep='') ,filename = pf)
h('Results of Different Metrics',3,filename = pf)
ss=""
i=0
for(ee in numeric_eval)
{
if(ee=='SI')
aa=paste("SC","-----",eval_full_name[[ee]])
else
aa=paste(ee,"-----",eval_full_name[[ee]])
for(nbb in c(nchar(aa):45))
aa=paste(aa," ",sep="")
ss=paste(ss,aa)
if(i%%2==1)
{
writeRmd(ss,filename=pf)
writeRmd("\n",filename=pf)
ss=""
}
i=i+1
}
if(length(numeric_eval)%%2==1)
{
writeRmd(ss,filename=pf)
writeRmd("\n",filename=pf)
}
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code=paste('
drawHeatmapRmd(list(t(table)),manyeval=TRUE,x_continuous=TRUE,k=as.integer(colnames(table)),x="Number of Clusters")',sep='') ,filename = pf)
}
if("KM"%in% pic_eval)
{
h('Kaplan-Meier Survival Curves',3,pf)
writeCode('',list(echo=FALSE,inlcude=TRUE,warning = FALSE,message = FALSE,error = FALSE),code=paste('\n'),closechunk = FALSE,filename = pf)
writeRmd(paste('par(mfrow=c(1,',n_pic_row,'))\n'),filename = pf)
s=paste("F_PINS_",pinsk[[1]],"_KM.RData",sep='')
writeRmd(paste('load("',s,'")\n',sep='') ,filename = pf)
writeRmd(paste('drawKMcurve(kmData,"Number of Clusters: ', pinsk[[1]] ,'")\n') ,filename = pf)
if(length(pinsk)>1)
{
s=paste("F_PINS_",pinsk[[2]],"_KM.RData",sep='')
writeRmd(paste('load("',s,'")\n',sep='') ,filename = pf)
writeRmd(paste('drawKMcurve(kmData,"Number of Clusters: ', pinsk[[2]] ,'")\n') ,filename = pf)
}
writeRmd(paste('```\n'),filename = pf)
}
}
render(pf, html_document())
if(is_report)
delfile(pf)
else
{
delfile(pf)
pf=paste(path,'/',strsplit(filename,".",fixed =TRUE)[[1]][1],".html",sep='')
delfile(pf)
}
}
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