MultiqcFile R6 Class

Contains methods for reading and displaying contents of the multiqc_data.json file output from MultiQC.

Super class

dracarys::File -> MultiqcFile

Methods

Public methods

• MultiqcFile$read()

• MultiqcFile$write()

• MultiqcFile$clone()

Inherited methods

• dracarys::File$bname()
• dracarys::File$initialize()
• dracarys::File$print()
• dracarys::File$type()

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Method read()

Reads the multiqc_data.json file output from MultiQC.

Usage

MultiqcFile$read(plot = FALSE, plot_names = NULL)

Arguments

plot

Return tibble with data for plots (def: FALSE).

plot_names

Names of plots to parse. Use "everything" if you wantz all the plotz.

Returns

A tidy tibble.

• label:

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Method write()

Writes a tidy version of the multiqc_data.json file output from MultiQC.

Usage

MultiqcFile$write(d, out_dir = NULL, prefix, out_format = "tsv", drid = NULL)

Arguments

d

Parsed object from self$read().

out_dir

Output directory.

prefix

Prefix of output file(s).

out_format

Format of output file(s) (one of 'tsv' (def.), 'parquet', 'both').

drid

dracarys ID to use for the dataset (e.g. wfrid.123, prid.456).

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Method clone()

The objects of this class are cloneable with this method.

Usage

MultiqcFile$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

if (FALSE) { # \dontrun{
x <- "/path/to/multiqc_data.json"
mqc <- MultiqcFile$new(x)
mqc_parsed <- mqc$read() # or read(mqc)
mqc$write(mqc_parsed, out_dir = tempdir(), prefix = "sample705", out_format = "tsv")
mqc_plots_parsed <- mqc$read(plot = TRUE, plot_names = "everything")
mqc$write(mqc_plots_parsed, out_dir = tempdir(), prefix = "sample705", out_format = "rds")
} # }