# Use this template to create a report that compares 2 pairwise comparisons of differential gene expression
CreateDdReport<-function(yml, overwrite=FALSE) {
# yml The yaml file or an yaml list defines the inputs and parameters of the analysis
library(awsomics);
library(gplots);
library(knitr);
library(rmarkdown);
library(yaml);
if (class(yml) == 'character') {
if (!file.exists(yml)) stop('Input file', yml, 'not found\n');
yml <- yaml::yaml.load_file(yml);
}
path<-yml$output;
if (!file.exists(path)) dir.create(path, recursive = TRUE);
if (yml$template$remote) {
if (!RCurl::url.exists(yml$template$location)) stop("Template Rmd file ', yml$input$template, ' not exists\n");
writeLines(RCurl::getURL(yml$template$location)[[1]], './DdReport.Rmd');
} else {
file.copy(yml$template$location, './DdReport.Rmd');
}
# save template and yaml file
file.copy('./DdReport.Rmd', paste(path, 'DdReport.Rmd', sep='/'));
writeLines(as.yaml(yml), paste(path, 'DdReport.yml', sep='/'));
wd<-getwd();
setwd(path);
errors<-list();
fn.md<-'DdReport.md';
if (file.exists(fn.md)) file.remove(fn.md);
# Run template, save error message
errors$knit<-try(knit('DdReport.Rmd', fn.md));
# Convert markdown file to html file
errors$render<-try(rmarkdown::render(fn.md, output_format="html_document", output_file="index.html", output_dir=path,
quiet=TRUE, envir=new.env()), silent=TRUE);
fld<-rev(strsplit(path, '/')[[1]])[1];
setwd('..');
# zip whole folder
fn.zip<-paste(fld, '.zip', sep='');
zip(fn.zip, fld, flag='-r0X', zip='zip');
file.rename(fn.zip, paste(fld, fn.zip, sep='/'));
setwd(wd);
list(output=path, message=errors);
}
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