Virusparies (version 1.1.0)

ExportVirusGt: ExportVirusGt: (Experimental) Export Graphical Tables

Description

ExportVirusGt allows the user to export graphical tables in different formats.

Usage

ExportVirusGt(
  gtable,
  filename = "table.docx",
  export_gt_obj = FALSE,
  path = NULL,
  create.dir = FALSE,
  ...
)

Value

A message indicating that export was successful.

Arguments

gtable

A graphical table object.

filename

Name of the output file (default: table.docx"). Make sure to provide an extension compatible with the output types: .html, .tex, .ltx, .rtf, .docx. If a custom save function is provided, the file extension is ignored.

export_gt_obj

(optional): If TRUE, exports the input data frame in .rds format with the same name as specified in filename (default: FALSE).

path

Path of the directory to save plot to: path and filename are combined to create the fully qualified file name (default: current corking directory).

create.dir

Whether to create new directories if a non-existing directory is specified in the filename or path (TRUE) or return an error (FALSE, default). If FALSE and run in an interactive session, a prompt will appear asking to create a new directory when necessary.

...

Pass any other options to the corresponding internal saving function.

Author

Sergej Ruff

Details

Export graphical tables (gt) generated by functions within the Virusparies package.

This feature is in an experimental phase and may not currently function as expected.

The exportVirusGt function utilizes the gt package for table manipulation and formatting.

For HTML output file names with .html or .htm extensions, an HTML document is generated using the gt package. Pass TRUE or FALSE to inline_css to include or exclude CSS styles inline (default is FALSE). Additional options can be passed through .... For RTF output file names with .rtf extension, an RTF file is created. Use the page_numbering option to control page numbering (default is none).

For image files, use .png for PNG and .pdf for PDF. The gt package relies on Google Chrome installation for PNG and PDF images. Pass options to webshot2::webshot() through .... Useful PNG options include zoom (default: 2) and expand (default: 5).

For LaTeX output file names with .tex, .ltx, or .rnw extensions, and .rtf for RTF, the corresponding documents are generated. No additional options available.

For .docx output, requires rmarkdown package.

When create.dir is set to TRUE, it generates a directory at the specified 'path' argument if the path doesn't already exist.

The optional export_gt_obj argument enables the user to export the data frame as a .rds file alongside the graphical table.

See Also

VirusHunterGatherer is available here: https://github.com/lauberlab/VirusHunterGatherer.

Examples

path <- system.file("extdata", "virushunter.tsv", package = "Virusparies")
vh_file <- ImportVirusTable(path)


# using first 10 rows of SRA_run,num_hits,bestquery,ViralRefSeq_E and Identity col.
vh_file_part <- vh_file[c(1:10),c(1,7,9,10,11)]

table <- VhgTabularRasa(vh_file_part,title = "first 10 rows of vh_file",subtitle =
"example for any table",names_ = c("Runs","Number of Contigs","Best Query Result",
"Reference E-Value","Reference Identity"))


# \donttest{

ExportVirusGt(gtable=table,filename="vh_parttable.docx",path=tempdir())

# }