In jasenfinch/metaboReports: Automated Report Generation For Metabolomics Analyses

knitr::opts_chunk$set(eval = FALSE)
library(knitr)
library(magrittr)
library(tibble)

Introduction

metaboReports provides a simple interface to enable automated, dynamic HTML report generation for results objects created from metabolomics analyses using the powerful R Markdown format. Detailed information on the R Markdown format can be found here.

Currently, report methods are available for:

tibble(
  `S4 class` = c('Binalysis','MetaboProfile','Analysis','Assignment','Workflow'),
  Package = c('[binneR](https://github.com/aberHRML/binneR)','[profilePro](https://github.com/jasenfinch/profilePro)','[metabolyseR](https://github.com/jasenfinch/metabolyseR)','[MFassign](https://github.com/jasenfinch/MFassign)','[metaboWorkflows](https://github.com/jasenfinch/metaboWorkflows)')
) %>%
  kable()

Basic usage

First load the library:

library(metaboReports)

The parameters for the report can be defined using the reportParameters() function as follows:

rp <- reportParameters(title = 'A metabolomics analysis',
                       investigator = 'Steve French',
                       sessionInfo = TRUE,
                       toc = TRUE,
                       path = '.')

The report can then be generated for the given object using the following:

report(analysis,rp)

This will create an output project directory named using the parameter title at the specified path. Within this directory, the files necessary to create the report will be generated and include an R Markdown file (.Rmd) containing the R and markdown code and a file containing the necessary data (reportData.rds). If report() is triggered from within RStudio, an RStudio project (.proj) file will also be created. Once these files are created, rmarkdown::render() is automatically called which will generate the final HTML report. Directories containing cached data and plot image files will also be created during this process.

jasenfinch/metaboReports documentation built on Nov. 19, 2021, 7:23 p.m.