xReport: Function to generate a html-formatted report

In XGR: Exploring Genomic Relations for Enhanced Interpretation Through Enrichment, Similarity, Network and Annotation Analysis

Description

xReport is supposed to generate a html-formatted report.

Usage

xReport(obj, rmd = NULL, output_format = NULL, output_file = NULL,
output_dir = NULL, quiet = T, verbose = T, ...)

Arguments

obj	an R object. Usually a S3-class object storing results such as an 'eTerm' object
rmd	the R markdown file. If NULL, the pre-prepared one in the directory 'inst/DynamicReport' of the XGR package will be used
output_format	the output format rendered from the R markdown file. If NULL, the output format is the first one defined within the R markdown file. The advanced use is to pass an output format object via rmarkdown::html_document()
output_file	the name of the output file. If NULL, the output filename will be based on the filename of R markdown file (extension replaced)
output_dir	the directory of the output file
quiet	the logic specifying whether to suppress printing of the pandoc command line
verbose	logical to indicate whether the messages will be displayed in the screen. By default, it sets to false for no display
...	additional parameters used in rmarkdown::render

Value

the message on the rendered output file and directory.

Note

none

See Also

xReport

Examples

# Load the XGR package and specify the location of built-in data
library(XGR)
RData.location <- "http://galahad.well.ox.ac.uk/bigdata/"


res <- xReport(eTerm)

# advanced use
output_format <-
rmarkdown::html_document(number_sections=T,theme="journal",
hightlight="espresso",code_folding="hide")
res <- xReport(eTerm, output_format=output_format)

XGR documentation built on June 18, 2019, 3:01 p.m.