writeHtmlReport {ngsReports} | R Documentation

## Write an HTML Summary Report

### Description

Compiles an HTML report using a supplied template

### Usage

    writeHtmlReport(
      fastqcDir,
      template,
      outDir,
      usePlotly = TRUE,
      species = "Hsapiens",
      gcType = c("Genome", "Transcriptome"),
      nOver = 30,
      targetsDF,
      overwrite = FALSE,
      quiet = TRUE
    )

### Arguments

`fastqcDir` | A directory containing zipped, or extracted FastQC reports
`template` | The template file which will be copied into `fastqcDir`
`outDir` | The directory to write the compiled document to
`usePlotly` | Generate interactive plots?
`species` | Species/closely related species of sequenced samples
`gcType` | Is the data "Transcriptomic" or "Genomic" in nature?
`nOver` | The maximum number of Overrepresented Sequences to show
`targetsDF` | A data.frame with at least two columns named `Filename` and `Label`. The filenames should match the original fastq files, and the labels should be simply alternative labels for these files for convenience.
`overwrite` | `logical`. Overwrite any previous copies of the template file in the destination directory
`quiet` | `logical`. Show or hide markdown output in the Console.

### Details

This will take a user supplied template, or the file supplied with the package and create an HTML summary of all standard FASTQC plots for all files in the supplied directory.

### Value

Silently returns `TRUE` and will output a compiled HTML file from the supplied Rmarkdown template file

### Examples

    ## Not run:
    packageDir <- system.file("extdata", package = "ngsReports")
    fileList <- list.files(packageDir, pattern = "fastqc.zip", full.names= TRUE)
    # Copy these files to tempdir() to avoid overwriting
    # any files in the package directory
    file.copy(fileList, tempdir(), overwrite = TRUE)
    writeHtmlReport(fastqcDir = tempdir())

    ## End(Not run)

[Package ngsReports version 1.8.1 Index]