# Use the ClReport.Rmd template to create a report of gene clustering analysis
CreateClReport<-function(yml) {
# yml The yaml file or an yaml list defines the inputs and parameters of the analysis
if (class(yml) == 'character') {
if (!file.exists(yml)) stop('Input file', yml, 'not found\n');
yml <- yaml::yaml.load_file(yml);
}
library(awsomics);
library(gplots);
library(knitr);
library(rmarkdown);
if (!file.exists(yml$output)) dir.create(yml$output, recursive = TRUE)
fn.temp<-paste(yml$output, 'ClReport.Rmd', sep='/');
if (yml$input$remote) {
if (!RCurl::url.exists(yml$input$template)) stop("Template Rmd file ', yml$input$template, ' not exists\n");
writeLines(RCurl::getURL(yml$input$template)[[1]], fn.temp);
} else {
file.copy(yml$input$template, fn.temp);
}
fn.html<-paste(yml$output, 'index.html', sep='/');
errors<-try(rmarkdown::render(fn.temp, output_format="html_document", output_file="index.html", output_dir=yml$output,
quiet=TRUE, envir=new.env()), silent=TRUE);
writeLines(yaml::as.yaml(yml), paste(yml$output, 'ClReport.yml', sep='/'));
zip(paste(yml$output, '.zip', sep=''), yml$output, "-rJ9X", zip='zip');
list(index=fn.html, zip=paste(yml$output, '.zip', sep=''), error=errors);
}
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