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

---

Summary Driver Table

summary.dt = fread(file.path(params$outdir, "summaryTable.txt"))
DT::datatable(summary.dt, escape=FALSE, options = list(scrollX = TRUE))

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="', expr.png.fn,'expr"',
                'src="',
            expr.png.fn,
                '" style="display:none;" width="45%" />',
                '<img', 'id="', gg.png.fn,'gg"', 'src="',
                gg.png.fn,
                '" style="display:none;" width="45%" />',
                '</p>'
            )
        )
        }   
    }

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="', cn.gallery.dt[gene_name == g, plot.fname],'cnv"','src="',
                    cn.gallery.dt[gene_name == g, plot.fname],
                    '" style="display:none;" width="100%" />',
                    '</p>'
            )
        )   
    }
}

---

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

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

gTrack

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