In jmw86069/platjam: Platform Jam, biological platform importers.

This document was prepared on r format(Sys.time(), "%a %b %d %X %Y").

Input is defined by a tabular file that contains coverage files and associated visualization options for each file.

Initialization of Rmarkdown

#
options("stringsAsFactors"=FALSE)

# process all arguments

# required file with input coverage files
coverage_file <- param$coverage_file;

# optional file to define anno_df
anno_file <- param$annofile;

# Render HTML page with this command:
# rmarkdown::render("Coverage_Heatmaps_07dec2022.Rmd", "html_document")
#
# log into bioinfo3, which contains magick C++ libraries
# working directory
# cd /ddn/gs1/project/nextgen/post/archer1/gokey_working/Copied_Intersections/042920_Stranded_Rmarkdown/ATAC_cov/081822_2235_DACs/Rmarkdown_18aug2022
# open R361 then run the render() function inside that R session

## Saved for reference, update JAM R packages
if (FALSE) {
   jampack <- c("jamba", "jamma", "multienrichjam",
      "venndir", "jamses", "platjam",
      "slicejam", "colorjam");
   for (i in jampack) {
      remotes::install_github(paste0("jmw86069/", i), upgrade="never")
   }
}

# /ddn/gs1/project/nextgen/post/archer1/gokey_working/Copied_Intersections/042920_Stranded_Rmarkdown/ATAC_cov/081822_2235_DACs
basepath <- file.path(
   "/ddn/gs1/project/nextgen/post/archer1",
   "gokey_working/Copied_Intersections/042920_Stranded_Rmarkdown",
   "ATAC_cov/081822_2235_DACs");
# slicejam
# 110619_ATAC_coverage_slice_1000s_v2.stats_mgm4_atac1.quantile_countsbatch.txt
sjfile <- file.path(basepath,
   "110619_ATAC_coverage_slice_1000s_v2.stats_mgm4_atac1.quantile_countsbatch.txt")

sjfile_txt_mtime <- file.info(sjfile)$mtime;

knitr::opts_chunk$set(
   cache=TRUE,
   autodep=TRUE,
   cache.extra=list(
      packageVersion("jamba"),
      # packageVersion("jamma"),
      packageVersion("jamses"),
      packageVersion("platjam"),
      packageVersion("venndir"),
      sjfile_txt_mtime,
      "cache_key_1"
   ),
   dev=c("png", "cairo_pdf"),
   # dev=c("png"),
   dev.args=list(
      cairo_pdf=list(family=c("Arial"))
   ),
   pdf.options(encoding="ISOLatin9.enc"),
   fig.height=8,
   fig.width=8,
   fig.align="center"
);
options("scipen"=12);
options("kable_styling_position"="left",
   "kable_styling_full_width"=FALSE,
   "kable_styling_bootstrap_options"=c("striped",
      "hover",
      "condensed",
      "responsive")
);

if (!suppressPackageStartupMessages(require(pacman))) {
   install.packages("pacman")
   require(pacman)
}
# load or install packages from Github as needed
p_load_gh("jmw86069/jamba");
p_load_gh("jmw86069/colorjam");
p_load_gh("jmw86069/jamma");
p_load_gh("jmw86069/genejam");
p_load_gh("jmw86069/venndir");
p_load_gh("jmw86069/jamses");
p_load_gh("jmw86069/platjam");
p_load_gh("jmw86069/jamsession");
p_load_gh("jmw86069/multienrichjam");

# load or install other required packages as needed
suppressPackageStartupMessages(p_load(SummarizedExperiment));
suppressPackageStartupMessages(p_load(ComplexHeatmap));
suppressPackageStartupMessages(p_load(igraph));

# load or install other required packages as needed
suppressPackageStartupMessages(p_load(kableExtra));
suppressPackageStartupMessages(p_load(ggplot2));