Virusparies (version 1.1.0)

ExportVirusDataFrame: ExportVirusDataFrame: Export processed hittables and summary stats data frames

Description

Export data frames generated by Virusparies functions.

Usage

ExportVirusDataFrame(
  df,
  file_name,
  dir_path = NULL,
  file_type = NULL,
  create_path = FALSE
)

Value

A message indicating that export was successful.

Arguments

df

A summary statistics or VirusHunterGatherer hittable data frame.

file_name

A character string naming the file, optionally including ".tsv" or ".csv" file extensions. If suffix is not provided, file_type will be used to determine the file type.

dir_path

A character string indicating the directory path where the file will be saved (default: current corking directory).

file_type

A character vector specifying the type of file to export. Can be "csv" or "tsv". If NULL and file_name does not specify a suffix, the function infers the file type based on the prefix in file_name.

create_path

Logical indicating whether to create the directory path specified in dir_path if it does not already exist (default: FALSE).

Author

Sergej Ruff

Details

Functions in the Virusparies package can generate both plots and new data frames. Data frames contain either summary statistics for contig length, E-value or identity in percentage or a processed hittable for example outlier or observations below threshold, when running VhgBoxplot.

Both types of data frames can be exported via ExportVirusDataFrame. Summary stats and hittables can be exported as CSV files or in TSV format, if the user prefers the file type used in VirusHunterGatherer hittables.

See Also

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

Examples

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


# generate a plot that returns both processed hittables (outlier) and summary stats
plot1 <- VhgBoxplot(file, x_column = "best_query", y_column = "ViralRefSeq_E")


# \donttest{

# export hittable as tsv (same format as input hittables)
ExportVirusDataFrame(df=plot1$outlier,file_name="outlier",file_type="tsv",
dir_path=tempdir())

# export summary stats as csv
ExportVirusDataFrame(df=plot1$summary_stats,file_name="summarystats",
file_type="csv",dir_path=tempdir())

# }