---
title: "R Notebook"
output: html_notebook
---


```{r}
setwd("Super specific/filepath/that/noone/else/has/")
# library(pheatmap)
heatmap <- function(df, xx) {
  xx <- read.csv("metadata_SRP070849.tsv", sep = "\t")
  df <- read.csv("SRP070849.tsv", sep = "\t")
  sums <- matrix(nrow = nrow(df), ncol = ncol(df) - 1)
  for (i in 1:nrow(sums)) {
    sums[i, ] <- sum(df[i, -1])
  }
  df2 <- df[which(df[, -1] >= 10), ]
  variances <- matrix(nrow = nrow(dds), ncol = ncol(dds) - 1)
  for (i in 1:nrow(dds)) {
    variances[i, ] <- var(dds[i, -1])
  }
  tmp <- quantile(variances, 0.75)
  df4 <- assay_df[which(variances > tmp), ]
  xx$refinebio_treatment <- substr(xx$refinebio_treatment, 0, 4)
  index1 <- which(colnames(xx) == "refinebio_accession_code")
  index2 <- which(colnames(xx) == "mutation")
  index3 <- which(colnames(xx) == "refinebio_treatment")
  xx2 <- xx[, c(index1, index2)]
  colnames(xx2) <- xx[, index3]
  plot <- pheatmap(df4, cluster_rows = TRUE, cluster_cols = TRUE, show_rownames = FALSE, annotation_col = xx2, main = "Annotated Heatmap", colorRampPalette(c("deepskyblue", "black", "yellow"))(25), scale = "row")
  png("SRP070849_heatmap_annotated.png")
  plot
  dev.off()
  # plot2=pheatmap(df4,cluster_rows=TRUE,cluster_cols=TRUE,show_rownames=FALSE,annotation_col=xx2, main = "Annotated Heatmap")
  # png("SRP070849_diff_version_heatmap_annotated.png")
  # plot2
  # dev.off()
}

heatmap()

# So we know what packages and versions were being used
sessionInfo()
```
