ggjs: ggjs

In mskilab/skitools: Various mskilab R utilties

ggjs

Description

Deploys a gGnome.js by downloaded the js / node source code from mskilab.com and then dumping json / csv files corresponding to the graph and coverage data.

Easiest way is to use pairs= argument which is a data.table with columns $pair, $jabba_rds, $cov_rds, $headline, $description where $headline is a character vector of the headline that will be displayed in the search bar and $description is the information that will be shown when the graph is loaded.

Takes gGraph objects or lists whose first item (or $graph) item is a gGraph, second optional item (or $cov) is a GRanges of coverage (where coverage data is specified by argument "field")

If arguments are named then these will be the name of the resulting object in the deployed gGnome.js app, otherwise they will be given default names (ie graph1, graph 2).

Dumps the app to a directory where to which user can navigate and deploy the app (instructions provided at runtime), default path is public_html/ggjs

Note: coverage should be less than 1e6 bins per file, if binsize is not NULL (default = 5000) then coverage data will be aggregated prior to dumping.

example argument: ggjs(path = gg, graph2 = list(gg2, cov2), list(cov = cov3, graph = gg3))

Usage

ggjs(
  ...,
  pairs = NULL,
  field = "ratio",
  path = "~/public_html/ggjs",
  binwidth = 5000,
  mc.cores = 1,
  web = TRUE,
  skip.dl = FALSE,
  clean.up = TRUE,
  force = FALSE,
  win = NULL,
  ggjs.url = "http://mskilab.com/gGnome.js/ggjs.tar.gz",
  verbose = TRUE
)

Arguments

...	gGnome objects of list
pairs	data.table with $pair, $jabba_rds, $cov_rds field to dump, can have optional fields $headline and $description
field	field of coverage GRanges that will be used to dump out the coverage data, default "ratio"
path	path to dump app to, this will also be the command that will be run to deloy the app ~/public_html/ggjs
web	whether to dump web version which will update datafiles.csv and dump files to json and coverage subfolders of path (FALSE)
binsize	binsize to aggregate coverage (default 5000)
skip.download	skip download (useful if dumping files to existing directory)

mskilab/skitools documentation built on Aug. 31, 2023, 1:13 p.m.