example_report.qmd

---
title: "Quality Control"
author: "Harvard Chan Bioinformatics Core"
date: "`r Sys.Date()`"
format:
  html:
    code-fold: true
    code-tools: true
    df-print: paged
    highlight-style: pygments
    number-sections: true
    self-contained: true
    theme: default
    toc: true
    toc-location: right
    toc-expand: false
params:
  # Fill this file with the right paths to nfcore output
  # Put hg38, mm10, mm39, or other
  # params_file: ../00_params/params.R 
  params_file: ../00_params/params-example.R # example data
  genome: hg38
  single_end: false
  factor_of_interest: sample_type
  project_file: ../information.R
  functions_file: ../00_libs/load_data.R
---

Template developed with materials from https://hbctraining.github.io/main/.

```{r, cache = FALSE, message = FALSE, warning=FALSE, eval = interactive()}
# This set up the working directory to this file so all files can be found
library(rstudioapi)
setwd(fs::path_dir(getSourceEditorContext()$path))
# NOTE: This code will check version, this is our recommendation, it may work
# .      other versions
stopifnot(R.version$major >= 4) # requires R4
if (compareVersion(R.version$minor, "3.1") < 0) warning("We recommend >= R4.3.1")
stopifnot(compareVersion(as.character(BiocManager::version()), "3.18") >= 0)
```

This code is in this ![](https://img.shields.io/badge/status-stable-green) revision.

```{r source_params, cache = FALSE, message = FALSE, warning=FALSE}
# 1. set up factor_of_interest parameter from parameter above or manually
#    this is used to color plots, it needs to be part of the metadata
factor_of_interest <- params$factor_of_interest
genome <- params$genome
single_end <- params$single_end
# 2. Set input files in this file
source(params$params_file)
# 3. If you set up this file, project information will be printed below and
# .   it can be reused for other Rmd files.
source(params$project_file)
# 4. Load custom functions to load data from coldata/metrics/counts
source(params$functions_file)
```

# Overview

-   Project: `r project`
-   PI: `r PI`
-   Analyst: `r analyst`
-   Experiment: `r experiment`


```{r load_libraries, cache = FALSE, message = FALSE, warning=FALSE}
library(tidyverse)
library(janitor)
library(knitr)
library(rtracklayer)
library(DESeq2)
library(DEGreport)
library(ggrepel)
# library(RColorBrewer)
library(DT)
library(pheatmap)
library(RColorBrewer)
library(ggprism)
library(grafify)
ggplot2::theme_set(theme_prism(base_size = 12))
# https://grafify-vignettes.netlify.app/colour_palettes.html
# NOTE change colors here if you wish
scale_colour_discrete <- function(...) {
  scale_colour_manual(...,
    values = as.vector(grafify:::graf_palettes[["kelly"]])
  )
}
scale_fill_discrete <- function(...) {
  scale_fill_manual(...,
    values = as.vector(grafify:::graf_palettes[["kelly"]])
  )
}

opts_chunk[["set"]](
  cache = FALSE,
  cache.lazy = FALSE,
  dev = c("png", "pdf"),
  error = TRUE,
  highlight = TRUE,
  message = FALSE,
  prompt = FALSE,
  tidy = FALSE,
  warning = FALSE,
  fig.height = 4)
```


```{r sanitize-datatable}
sanitize_datatable <- function(df, ...) {
  # remove dashes which cause wrapping
  DT::datatable(df, ...,
    rownames = gsub("-", "_", rownames(df)),
    colnames = gsub("-", "_", colnames(df))
  )
}
```

# Conclusions

# Methods

Add methods.

## R package references

```{r citations, results='asis'}
citation("ggplot2")
```

## R session

List and version of tools used for the QC report generation.

```{r}
sessionInfo()
```