Loads one or more MultiQC reports into a data frame

Loads one or more MultiQC reports into a data frame

load_multiqc(
  paths,
  plots = NULL,
  find_metadata = function(...) {     list() },
  plot_parsers = list(),
  sections = "general"
)

Arguments

paths

A string vector of filepaths to multiqc_data.json files

plots

A string vector, each of which contains the ID of a plot you want to include in the output. You can use list_plots() to help here.

find_metadata

A single function that will be called with a sample name and the parsed JSON for the entire report and returns a named list of metadata fields for the sample. Refer to the vignette for an example.

plot_parsers

Advanced. A named list of custom parser functions. The names of the list should correspond to plotly plot types, such as "xy_line", and the values should be functions that return a named list of named lists. For the return value, the outer list is named by the sample ID, and the inner list is named by the name of the column. Refer to the source code for some examples.

sections

A string vector of zero or more sections to include in the output. Each section can be:

"plot"

Parse plot data. Note that you should also provide a list of plots via the plots argument

"general"

parse the general stat section

"raw"

Parse the raw data section

This defaults to 'general', which tends to contain the most useful statistics

Value

A tibble (data.frame subclass) with QC data and metadata as columns, and samples as rows. Columns are named according to the respective section they belong to, and will always be listed in the following order:

metadata.X

This column contains metadata for this sample. By default this is only the sample ID, but if you have provided the find_metadata argument, there may be more columns.

general.X

This column contains a generally useful summary statistic for each sample

plot.X

This column contains a data frame of plot data for each sample. Refer to the plot parsers documentation (ie the parse_X functions) for more information on the output format.

raw.X

This column contains a raw summary statistic or value relating to each sample

See also

parse_xyline_plot() parse_bar_graph()

Examples

load_multiqc(system.file("extdata", "wgs/multiqc_data.json", package = "TidyMultiqc"))
#> # A tibble: 6 × 165
#>   metadata.sam…¹ gener…² gener…³ gener…⁴ gener…⁵ gener…⁶ gener…⁷ gener…⁸ gener…⁹
#>   <chr>            <dbl>   <dbl>   <dbl>   <int>   <int>   <dbl>   <dbl>   <dbl>
#> 1 P4107_1003      8.68e8  8.48e8    97.6      40     365    41.4    92.3    92.2
#> 2 P4107_1004      1.00e9  9.85e8    98.2      46     363    41.0    92.3    92.2
#> 3 P4107_1005      9.75e8  9.56e8    98.0      45     368    41.2    92.3    92.2
#> 4 P4107_1002      8.66e8  8.47e8    97.8      40     367    41.3    92.3    92.2
#> 5 P4107_1006      9.12e8  8.95e8    98.1      43     362    41.3    92.3    92.2
#> 6 P4107_1001      7.72e8  7.51e8    97.3      36     358    41.4    92.3    92.2
#> # … with 156 more variables: general.10_x_pc <dbl>, general.30_x_pc <dbl>,
#> #   general.50_x_pc <dbl>, general.genome <chr>,
#> #   general.number_of_variants_before_filter <dbl>,
#> #   general.number_of_known_variants_brie_non_empty_id <dbl>,
#> #   general.number_of_known_variants_brie_non_empty_id_percent <dbl>,
#> #   general.number_of_effects <dbl>, general.genome_total_length <dbl>,
#> #   general.genome_effective_length <dbl>, general.change_rate <dbl>, …