In mskilab/casereport: casereport: Whole-genome + transcription based report for cancer genomes

---

title: Whole genome/transcriptome sequencing of r params$pair, r paste(ifelse(grepl("^[aeiou]", params$tumor_type, ignore.case = T), "an", "a"), params$tumor_type)

---

## global code chunk option
knitr::opts_chunk$set(
    collapse = TRUE,
    fig.width = 8,
    fig.height = 8,
    message = FALSE,
    warning = FALSE,
    echo = FALSE)

## hopefully make skidb standard asap
library(gGnome)
library(gTrack)
library(skidb)
library(ggplot2)
library(ggforce)
library(kableExtra)
library(hwriter)
library(htmlwidgets)
library(svglite)
library(slickR)
library(plotly)
library(shiny)
message("Loaded Packages")

summary.list = readRDS(normalizePath(file.path(params$outdir, "summary.rds")))
message("Loaded gGraph")

```{css,echo=FALSE} button.btn.collapsed:before { content:'+' ; display:block; width:15px; } button.btn:before { content:'-' ; display:block; width:15px; }

```r

knitr::knit_hooks$set(dropAboveCol=function(before, options, envir) {
    if (before) {
        paste(
            '<p>',
paste('<button class="btn btn-primary collapsed" id="BT-', options$label,'" data-toggle="collapse" data-target="#',options$label,'">',sep=""),
'</button>',
'</p>',
paste('<div class="collapse" id="',options$label,'">',sep=""), sep = "\n")
    }
})

#For sections to be expanded by default, use this one. 
knitr::knit_hooks$set(dropAboveExp=function(before, options, envir) {
    if (before) {
        paste(
            '<p>',
paste('<button class="btn btn-primary" data-toggle="collapse" data-target="#',options$label,'"aria-expanded="true">',sep=""),
'</button>',
'</p>',
paste('<div class="collapse in" id="',options$label,'">',sep=""),sep = "\n")
    }
})

knitr::knit_hooks$set(dropBelow=function(before, options, envir) {
    if (!before) {
      paste("</div>", sep="\n")
    }
})

---

r paste(params$pair, params$tumor_type, sep = ", ")

Purity/ploidy

Estimated purity: r format(summary.list$purity, digits = 2)

Estimated ploidy: r format(summary.list$ploidy, digits = 2)

SCNA

Copy number alterations (CNA) are defined as CN at most 0.5 times ploidy (deletions) or at least 1.5 times ploidy (amplifications).

Percent of genome with CNA: r format(round(summary.list$cna_frac * 100, 2), nsmall = 2)%

Total amplifications (Mbp): r format(round(summary.list$amp_mbp, 2), nsmall = 2)

Total deletions (Mbp): r format(round(summary.list$del_mbp, 2), nsmall = 2)

Total CNA (Mbp): r format(round(summary.list$cna_mbp, 2), nsmall = 2)

Junction burden

The total junction burden is r summary.list$junction_burden.

SNV

Total number of somatic SNV/INDELs: r format(round(summary.list$mut_count, 0), nsmall = 0)

Tumor Mutation Burden (TMB): r format(round(summary.list$mut_per_mbp, 2), 2) per Mbp

print(params$outdir)

---

Summary Driver Table

summary.dt = fread(file.path(params$outdir, "summaryTable.txt"))
expr.hist.dt = fread(file.path(params$outdir, "expr.histograms.txt"))
expr.slickr.dt = fread(file.path(params$outdir, "expr.gallery.txt"))
cn.gallery.dt = fread(file.path(params$outdir, "cn.gallery.txt"))
fusions.gallery.dt = fread(file.path(params$outdir, "fusions.driver.txt"))
driver.mutations.dt = fread(file.path(params$outdir, "driver.mutations.txt"))


basebutton=paste('<input type="button" onclick="openTabset"',';" value="thisValue" />',sep="'")
ExpSequences=c("overexpression","underexpression")
CnvSequences=c("amp","hetdel","loh","homdel")
SnvSequences=c("missense")

for(i in 1:nrow(summary.dt)){
  g=gsub(".*/gene/","",summary.dt$gene[i])
  g=gsub(" target.*$","",g)
  if(grepl("expression",summary.dt$type[i])){
    for(val in ExpSequences){
      if(grepl(val,summary.dt$type[i])){
        summary.dt$type[i]=gsub(val,basebutton,summary.dt$type[i])
        summary.dt$type[i]=gsub("thisValue",val,summary.dt$type[i])
        forAction=paste0("showImg('",g,".expr');showImg('",g,".gg')",";showImg('",g,".expt')",";showHeader('expheader','divEXP')")
        summary.dt$type[i]=gsub('openTabset',forAction,summary.dt$type[i])
      }
    }
  }
  if(grepl("amp|hetdel|homdel|loh",summary.dt$type[i])){
    for(val in CnvSequences){
      if(grepl(val,summary.dt$type[i])){
        summary.dt$type[i]=gsub(val,basebutton,summary.dt$type[i])
        summary.dt$type[i]=gsub("thisValue",val,summary.dt$type[i])
        forAction=paste0("showImg('",g,".cnv')",";showImg('",g,".cnvtt')",";showHeader('cnvheader','divCNV')")
        summary.dt$type[i]=gsub('openTabset',forAction,summary.dt$type[i])
      }
    }
  }
  if(grepl("fusion",summary.dt$type[i])){
        summary.dt$type[i]=gsub("fusion",basebutton,summary.dt$type[i])
        summary.dt$type[i]=gsub("thisValue","fusion",summary.dt$type[i])

        forAction=paste0("showImg('",fusions.gallery.dt[driver.name == g, driver.name],".fus')",";showImg('",g,".fust')",";showHeader('fusheader','divFUS')")
        summary.dt$type[i]=gsub('openTabset',forAction,summary.dt$type[i])
  }

  if(grepl("missense",summary.dt$type[i])){
        summary.dt$type[i]=gsub("missense",basebutton,summary.dt$type[i])
        summary.dt$type[i]=gsub("thisValue","missense",summary.dt$type[i])
        forAction=paste0("showImg('",driver.mutations.dt[gene == g, gene],".snvt')",";showHeader('snvheader','divSNV')")
        summary.dt$type[i]=gsub("openTabset",forAction,summary.dt$type[i])
  }
  if(grepl("proximity",summary.dt$type[i])){
        summary.dt$type[i]=gsub("proximity",basebutton,summary.dt$type[i])
        summary.dt$type[i]=gsub("thisValue","proximity",summary.dt$type[i])

        forAction=paste0("showImg('",g,".prox')")
        summary.dt$type[i]=gsub('openTabset',forAction,summary.dt$type[i])
  }
  summary.dt$type[i]=gsub(", ,",",",summary.dt$type[i])
}
DT::datatable(summary.dt, escape=FALSE, options = list(scrollX = TRUE))

driver.genes.cnv = fread(file.path(params$outdir, "driver.genes.cnv.txt"))
driver.genes.cnv$min_normalized_cn=unlist(lapply(driver.genes.cnv$min_normalized_cn,FUN=signif,digits=4))
driver.genes.cnv$max_normalized_cn=unlist(lapply(driver.genes.cnv$max_normalized_cn,FUN=signif,digits=4))
driver.genes.cnv$expr.quantile=unlist(lapply(driver.genes.cnv$expr.quantile,FUN=signif,digits=4))

cat('<div class="divScroll" id="divCNV" style="display:none">')
cat('<table class="display dataTable no-footer table table-condensed" aria-describedby="CNV_Table">')
headerline='<tr id="cnvheader" style="display:none">'
for(i in colnames(driver.genes.cnv)){
  thisH=paste0('<th>',i,'</th>')
  headerline=paste0(headerline,thisH)
}
cat(paste0(headerline,'</tr>'))

if(nrow(driver.genes.cnv)>0){
 for(i in 1:nrow(driver.genes.cnv)){
  rLine=paste0('<tr class="odd" id="',driver.genes.cnv$gene[i],'.cnvtt" style="display:none">')
  for(j in 1:ncol(driver.genes.cnv)){
    thisL=paste0('<td>',as.vector(as.matrix(driver.genes.cnv)[i,j]),'</td>')
    rLine=paste0(rLine,thisL)
  }
  cat(paste0(rLine,'</tr>'))
 }
cat('</table>') 
}else{
cat('No driver genes with CNVs')   
    }
cat('</div>')

cn.gallery.dt = fread(file.path(params$outdir, "cn.gallery.txt"))
if (nrow(cn.gallery.dt) > 0) {
    for (g in cn.gallery.dt[, gene_name]) {
        cat(
            paste0('<p>',
                    '<img',' id="', g,'.cnv"',' src="',
                    cn.gallery.dt[gene_name == g, plot.fname],
                    '" style="display:none;" width="100%" />',
                    '</p>'
            )
        )   
    }
}

driver.genes.expr = fread(file.path(params$outdir, "driver.genes.expr.txt"))
driver.genes.expr$min_normalized_cn=unlist(lapply(driver.genes.expr$min_normalized_cn,FUN=signif,digits=4))
driver.genes.expr$max_normalized_cn=unlist(lapply(driver.genes.expr$max_normalized_cn,FUN=signif,digits=4))
driver.genes.expr$expr.quantile=unlist(lapply(driver.genes.expr$expr.quantile,FUN=signif,digits=4))
if (driver.genes.expr[,.N] > 0){
    driver.genes.expr$zscore=unlist(lapply(driver.genes.expr$zscore,FUN=signif,digits=4))
    driver.genes.expr = driver.genes.expr[order(-abs(zscore))] #  sort by Z-score
}

if(nrow(driver.genes.expr)>0){
  cat('<div class="divScroll" id="divEXP" style="display:none">')
  cat('<table class="display dataTable no-footer table table-condensed" aria-describedby="EXP_Table">')
  headerline='<tr id="expheader" style="display:none">'
  for(i in colnames(driver.genes.expr)){
    thisH=paste0('<th>',i,'</th>')
    headerline=paste0(headerline,thisH)
  }
  cat(paste0(headerline,'</tr>'))

  for(i in 1:nrow(driver.genes.expr)){
    rLine=paste0('<tr class="odd" id="',driver.genes.expr$gene[i],'.expt" style="display:none">')
    for(j in 1:ncol(driver.genes.expr)){
      thisL=paste0('<td>',as.vector(as.matrix(driver.genes.expr)[i,j]),'</td>')
      rLine=paste0(rLine,thisL)
    }
    cat(paste0(rLine,'</tr>'))
  }

  cat('</table>')
  cat('</div>')
}

expr.hist.dt = fread(file.path(params$outdir, "expr.histograms.txt"))
cool.exp = fread(paste0(params$outdir, "/", "rna.change.txt"))
expr.slickr.dt = fread(file.path(params$outdir, "expr.gallery.txt"))
cat("\n")
valid.genes = intersect(expr.hist.dt[, gene], expr.slickr.dt[, gene_name])
for (g in valid.genes) {
    expr.png.fn = expr.hist.dt[gene == g, expr.hist.fname][1]
    gg.png.fn = expr.slickr.dt[gene_name == g, plot.fname][1]
    if (file.exists(expr.png.fn) & file.exists(gg.png.fn)) {
         cat(
            paste0(
                '<p float="left">',
                '<img ', 'id="', g,'.expr"',
                ' src="',
            expr.png.fn,
                '" style="display:none;" width="45%" />',
                '<img', ' id="', g,'.gg"', ' src="',
                gg.png.fn,
                '" style="display:none;" width="45%" />',
                '</p>'
            )
        )
        }   
    }

driver.fusions.fname = file.path(params$outdir, "fusions.driver.txt")
if (file.exists(driver.fusions.fname)) {
   driver.fusions.dt = fread(driver.fusions.fname)
   if (nrow(driver.fusions.dt)) {
      driver.fusions.cols = intersect(c("genes", "walk.id", "driver.name", "chroms", "maxcn", "total.aa", "gene.pc", "ev.id", "ev.type"), colnames(driver.fusions.dt))
      dat = driver.fusions.dt[, ..driver.fusions.cols]
   }
}

fusions.gallery.dt = fread(file.path(params$outdir, "fusions.driver.txt"))
summary.dt = fread(file.path(params$outdir, "summaryTable.txt"))
driverGenes=summary.dt$gene
driverGenes=sapply(driverGenes,function(x) gsub(".*/gene/","",x))
driverGenes=sapply(driverGenes,function(x) sub(" target.*$","",x))

if(any(fusions.gallery.dt$genes %in% driverGenes)){
  cat('<div class="divScroll" id="divFUS" style="display:none">')
  cat('<table class="display dataTable no-footer table table-condensed" aria-describedby="FUS_Table">')
  headerline='<tr id="fusheader" style="display:none">'
  for(i in colnames(driver.genes.expr)){
   thisH=paste0('<th>',i,'</th>')
   headerline=paste0(headerline,thisH)
  }
  cat(paste0(headerline,'</tr>'))


  for(i in 1:nrow(driver.genes.expr)){
   if(driver.fusions.dt$driver.name[i] %in% driverGenes){
    for(j in 1:ncol(dat)){
     thisL=paste0('<td>',as.vector(as.matrix(dat)[i,j]),'</td>')
     rLine=paste0(rLine,thisL)
   }
   cat(paste0(rLine,'</tr>'))
   }
  }

  cat('</table>')
  cat('</div>')
}

if (nrow(fusions.gallery.dt) > 0) {
      for (g in fusions.gallery.dt[, genes]) {
        if(g %in% driverGenes){
            cat(
                paste0('<p>',
                       '<img', ' id="',paste0(fusions.gallery.dt[genes == g, driver.name],'.fus'),'" src="',
                       fusions.gallery.dt[genes == g, plot.fname],
                       '" style="display:none;" width="75%" />',
                       '</a>',
                       '</p>'
                       )
            )
        }
        }
    }

proximity.gallery.dt = fread(paste0(params$outdir, "/", "proximity.gallery.txt"))
expr.histograms.dt = fread(paste0(params$outdir, "/", "expr.histograms.txt"))
    if (nrow(proximity.gallery.dt) > 0) {
      gns = intersect(proximity.gallery.dt$gene, expr.histograms.dt$gene)
        for (g in gns) {
            cat(
                paste0('<p>',
                       '<img', ' id="',paste0(g,'.prox'),'" src="',
                       proximity.gallery.dt[gene == g, plot.fname],
                       '" style="display:none;" width="75%" />',
                       '</a>',
                       '</p>'
                       )
            )
        }
    }

if(nrow(driver.mutations.dt)>0){
driver.mutations.dt$Tier=as.character(driver.mutations.dt$Tier)
driver.mutations.dt[is.na(driver.mutations.dt$Tier),]$Tier="Undefined"

cat('<div class="divScroll" id="divSNV" style="display:none">')
cat('<table class="display dataTable no-footer table table-condensed" aria-describedby="SNV_Table">')
headerline='<tr id="snvheader" style="display:none">'
for(i in colnames(driver.mutations.dt)){
  thisH=paste0('<th>',i,'</th>')
  headerline=paste0(headerline,thisH)
}
cat(paste0(headerline,'</tr>'))


for(i in 1:nrow(driver.mutations.dt)){
  rLine=paste0('<tr class="odd" id="',driver.mutations.dt$gene[i],'.snvt" style="display:none">')
  for(j in 1:ncol(driver.mutations.dt)){
    thisL=paste0('<td>',as.vector(as.matrix(driver.mutations.dt)[i,j]),'</td>')
    rLine=paste0(rLine,thisL)
  }
  cat(paste0(rLine,'</tr>'))
}

cat('</table>')

}

---

Summary Surface Table

summary.dt = fread(file.path(params$outdir, "summarySurfaceTable.txt"))
expr.hist.dt = fread(file.path(params$outdir, "surface.expr.histograms.txt"))
expr.slickr.dt = fread(file.path(params$outdir, "surface.expr.gallery.txt"))
cn.gallery.dt = fread(file.path(params$outdir, "surface.cn.gallery.txt"))

basebutton=paste('<input type="button" onclick="openTabset"',';" value="thisValue" />',sep="'")
ExpSequences=c("overexpression","underexpression")
CnvSequences=c("amp","hetdel","loh","homdel")
SnvSequences=c("missense")

if(nrow(summary.dt)>1){
for(i in 1:nrow(summary.dt)){
  g=gsub(".*/gene/","",summary.dt$gene[i])
  g=gsub(" target.*$","",g)
  if(grepl("expression",summary.dt$type[i])){
    for(val in ExpSequences){
      if(grepl(val,summary.dt$type[i])){
        summary.dt$type[i]=gsub(val,basebutton,summary.dt$type[i])
        summary.dt$type[i]=gsub("thisValue",val,summary.dt$type[i])
        forAction=paste0("showImg('",g,".expr');showImg('",g,".gg')",";showImg('",g,".sexpt')",";showHeaderSurface('sexpheader','SdivEXP')")
        summary.dt$type[i]=gsub('openTabset',forAction,summary.dt$type[i])
      }
    }
  }
  if(grepl("amp|hetdel|homdel|loh",summary.dt$type[i])){
    for(val in CnvSequences){
      if(grepl(val,summary.dt$type[i])){
        summary.dt$type[i]=gsub(val,basebutton,summary.dt$type[i])
        summary.dt$type[i]=gsub("thisValue",val,summary.dt$type[i])
        forAction=paste0("showImg('",g,".cnv')",";showImg('",g,".scnvtt')",";showHeaderSurface('scnvheader','SdivCNV')")
        summary.dt$type[i]=gsub('openTabset',forAction,summary.dt$type[i])
      }
    }
  }
    if(grepl("fusion",summary.dt$type[i])){
        summary.dt$type[i]=gsub("fusion",basebutton,summary.dt$type[i])
        summary.dt$type[i]=gsub("thisValue","fusion",summary.dt$type[i])

        forAction=paste0("showImg('",fusions.gallery.dt[driver.name == g, driver.name],".fus')",";showImg('",g,".fust')",";showHeaderSurface('sfusheader','SdivFUS')")
        summary.dt$type[i]=gsub('openTabset',forAction,summary.dt$type[i])
  }
  summary.dt$type[i]=gsub(", ,",",",summary.dt$type[i])
}
DT::datatable(summary.dt, escape=FALSE, options = list(scrollX = TRUE))
}

surface.genes.cnv = fread(file.path(params$outdir, "surface.genes.cnv.txt"))
surface.genes.cnv$min_normalized_cn=unlist(lapply(surface.genes.cnv$min_normalized_cn,FUN=signif,digits=4))
surface.genes.cnv$max_normalized_cn=unlist(lapply(surface.genes.cnv$max_normalized_cn,FUN=signif,digits=4))
surface.genes.cnv$expr.quantile=unlist(lapply(surface.genes.cnv$expr.quantile,FUN=signif,digits=4))

if(nrow(surface.genes.cnv)>1){
cat('<div class="divScroll" id="SdivCNV" style="display:none">')
cat('<table class="display dataTable no-footer table table-condensed" aria-describedby="SCNV_Table">')
headerline='<tr id="scnvheader" style="display:none">'
for(i in colnames(surface.genes.cnv)){
  thisH=paste0('<th>',i,'</th>')
  headerline=paste0(headerline,thisH)
}
cat(paste0(headerline,'</tr>'))


for(i in 1:nrow(surface.genes.cnv)){
  rLine=paste0('<tr class="odd" id="',surface.genes.cnv$gene[i],'.scnvtt" style="display:none">')
  for(j in 1:ncol(driver.genes.cnv)){
    thisL=paste0('<td>',as.vector(as.matrix(surface.genes.cnv)),'</td>')
    rLine=paste0(rLine,thisL)
  }
  cat(paste0(rLine,'</tr>'))
}

cat('</table>')
cat('</div>')
}

cn.gallery.dt = fread(file.path(params$outdir, "surface.cn.gallery.txt"))
if (nrow(cn.gallery.dt) > 0) {
    for (g in cn.gallery.dt[, gene_name]) {
        cat(
            paste0('<p>',
                    '<img',' id="', g,'.cnv"',' src="',
                    cn.gallery.dt[gene_name == g, plot.fname],
                    '" style="display:none;" width="100%" />',
                    '</p>'
            )
        )   
    }
}

surface.genes.expr = fread(file.path(params$outdir, "surface.genes.expr.txt"))
if (surface.genes.expr[,.N] > 0){
    surface.genes.expr$min_normalized_cn=unlist(lapply(surface.genes.expr$min_normalized_cn,FUN=signif,digits=4))
    surface.genes.expr$max_normalized_cn=unlist(lapply(surface.genes.expr$max_normalized_cn,FUN=signif,digits=4))
    surface.genes.expr$expr.quantile=unlist(lapply(surface.genes.expr$expr.quantile,FUN=signif,digits=4))
    surface.genes.expr$expr = factor(surface.genes.expr$expr, c('over', 'under', ''))
    surface.genes.expr$zscore=unlist(lapply(surface.genes.expr$zscore,FUN=signif,digits=4))
    surface.genes.expr = surface.genes.expr[order(-abs(zscore))] #  sort by Z-score
    surface.genes.expr = surface.genes.expr[order(expr, -min_cn, -abs(zscore))] # sort to show over expressed, and then underexpressed. Whithin over-expressed we show highest CN first and for each CN we sort by Z-score
}

if(nrow(surface.genes.expr)>0){
  cat('<div class="divScroll" id="SdivEXP" style="display:none">')
  cat('<table class="display dataTable no-footer table table-condensed" aria-describedby="SEXP_Table">')
  headerline='<tr id="sexpheader" style="display:none">'
  for(i in colnames(surface.genes.expr)){
    thisH=paste0('<th>',i,'</th>')
    headerline=paste0(headerline,thisH)
  }
  cat(paste0(headerline,'</tr>'))


  for(i in 1:nrow(surface.genes.expr)){
    rLine=paste0('<tr class="odd" id="',surface.genes.expr$gene[i],'.sexpt" style="display:none">')
    for(j in 1:ncol(driver.genes.expr)){
      thisL=paste0('<td>',as.vector(as.matrix(surface.genes.expr)[i,j]),'</td>')
      rLine=paste0(rLine,thisL)
    }
    cat(paste0(rLine,'</tr>'))
  }

  cat('</table>')
  cat('</div>')
}

expr.hist.dt = fread(file.path(params$outdir, "surface.expr.histograms.txt"))
cool.exp = fread(paste0(params$outdir, "/", "surface.rna.change.txt"))
expr.slickr.dt = fread(file.path(params$outdir, "surface.expr.gallery.txt"))
cat("\n")
valid.genes = intersect(expr.hist.dt[, gene], expr.slickr.dt[, gene_name])
for (g in valid.genes) {
    expr.png.fn = expr.hist.dt[gene == g, expr.hist.fname][1]
    gg.png.fn = expr.slickr.dt[gene_name == g, plot.fname][1]
    if (file.exists(expr.png.fn) & file.exists(gg.png.fn)) {
         cat(
            paste0(
                '<p float="left">',
                '<img ', 'id="', g,'.expr"',
                ' src="',
            expr.png.fn,
                '" style="display:none;" width="45%" />',
                '<img', ' id="', g,'.gg"', ' src="',
                gg.png.fn,
                '" style="display:none;" width="45%" />',
                '</p>'
            )
        )
        }   
    }

driver.fusions.fname = file.path(params$outdir, "fusions.driver.txt")
if (file.exists(driver.fusions.fname)) {
   driver.fusions.dt = fread(driver.fusions.fname)
   if (nrow(driver.fusions.dt)) {
      driver.fusions.cols = intersect(c("genes", "walk.id", "driver.name", "chroms", "maxcn", "total.aa", "gene.pc", "ev.id", "ev.type"), colnames(driver.fusions.dt))
      dat = driver.fusions.dt[, ..driver.fusions.cols]
   }
}

summary.dt = fread(file.path(params$outdir, "summarySurfaceTable.txt"))
driverGenes=summary.dt$gene
driverGenes=sapply(driverGenes,function(x) gsub(".*/gene/","",x))
driverGenes=sapply(driverGenes,function(x) sub(" target.*$","",x))

if(any(fusions.gallery.dt$driver.name %in% driverGenes)){
  cat('<div class="divScroll" id="SdivFUS" style="display:none">')
  cat('<table class="display dataTable no-footer table table-condensed" aria-describedby="SFUS_Table">')
  headerline='<tr id="sfusheader" style="display:none">'
  for(i in colnames(dat)){
   thisH=paste0('<th>',i,'</th>')
   headerline=paste0(headerline,thisH)
  }
  cat(paste0(headerline,'</tr>'))


  for(i in 1:nrow(fusions.gallery.dt)){
   rLine=paste0('<tr class="odd" id="',driver.fusions.dt$driver.name[i],'.fust" style="display:none">')
   if(driver.fusions.dt$driver.name[i] %in% driverGenes){
    for(j in 1:ncol(dat)){
     thisL=paste0('<td>',as.vector(as.matrix(dat)[i,j]),'</td>')
     rLine=paste0(rLine,thisL)
   }
   cat(paste0(rLine,'</tr>'))
   }
  }

  cat('</table>')
  cat('</div>')
}

if (nrow(fusions.gallery.dt) > 0) {
        for (g in fusions.gallery.dt[, genes]) {
          if(!(g %in% driverGenes)){
            cat(
                paste0('<p>',
                       '<img', ' id="',paste0(fusions.gallery.dt[genes == g, driver.name],'.fus'),'" src="',
                       fusions.gallery.dt[genes == g, plot.fname],
                       '" style="display:none;" width="75%" />',
                       '</a>',
                       '</p>'
                       )
            )
          }
        }
    }

---

Whole genome view {.tabset .tabset-fade .tabset-pills}

cat('<div id="gtrack" class="section level2">')

gTrack

wzxhzdk:21