drighelli / easyreporting

easyreporting

easyreporting

This package implements an S4 class for facilitating the automation of creation of rmarkdown files inside other packages/software.

Installation

At the current status, the easyiest way to install it is through devtools:

if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")
    
devtools::install_github("drighelli/easyreporting", build_vignettes=TRUE)

Long documentations

The easyreporting package comes with two vignettes to guide the user on its usage:

Bioinformatics usage

The first one has been designed for illustrating the easy way to implement and use easyreporting during bioinformatics analysis.

vignette("bio_usage", package="easyreporting")

Standard usage

This one is for illustrating a standard usage of the package showing all its multiple functionalities.

vignette("standard_usage", package="easyreporting")

easyreporting's Issues

easyreporting::erGUIVolcano() error

In easyreporting::erGUIVolcano() the server file needs to be updated in R 4.1 version

what you have right now:
mkdCodeChunkTitledCommented(object=er, title="Volcano Plot", level=1, codeMsg=paste0(" degs <- readRDS(\"degs.RDS\")\nVolcanoPlot(degs=degs, threshold=", threshold,")"), commentMsg=comment, sourceFilesList=system.file("script/plotFunctions.R", package="easyreporting"))

what the code needs to be changed too:
mkdCodeChunkTitledCommented(object=er, title="Volcano Plot", level=1, code=paste0(" degs <- readRDS(\"degs.RDS\")\nVolcanoPlot(degs=degs, threshold=", threshold,")"), comment=comment, sourceFilesList=system.file("script/plotFunctions.R", package="easyreporting"))

The second code chunk also works in R 4.0.5 too.

Please add easyreporting::erGUIVolcano() to R 4.0.5