SequenzaSummary.Rmd

---
title: "Sequenza Run: gamma effect"
output: pdf_document
params:
  sample: "TEST"
  summaryImage: ""
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo=FALSE, dev = "cairo_pdf", dpi = 200)

library(knitr)
library(grid)
library(optparse)
library(png)
```

```{r title, echo=FALSE, results='asis'}
  cat("#", (paste0("Sample: ",params$sample)), "\n")
```

```{r summary_plot, echo=FALSE, warning=FALSE}
 img <- readPNG(params$summaryImage, native = TRUE)
 grid.raster(img, interpolate = TRUE)

```

```{r gamma_plots, echo=FALSE, warning=FALSE}

 DIRS<-dir("gammas/")
 DIRS<-as.integer(DIRS)
 BY_INCREASE = order(DIRS)

 gamma = DIRS[BY_INCREASE]
 for (g in 1:length(gamma)) {
  grid.newpage()
  img <- readPNG(paste0("gammas/",gamma[g],"/",params$sample,"_gammaPanel_",gamma[g],".png"), native = TRUE)
  grid.raster(img, interpolate = TRUE)
 }

```