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Plot read depth for multiOmicDataSet

Source: R/plot_read_depth.R
plot_read_depth.multiOmicDataSet.Rd

Plot read depth for multiOmicDataSet

Arguments

count_type

the type of counts to use. Must be a name in the counts slot (names(moo@counts)).

sub_count_type

used if count_type is a list in the counts slot: specify the sub count type within the list. Must be a name in names(moo@counts[[count_type]]).

sample_id_colname

column in sample metadata containing sample IDs.

group_colname

sample metadata column used to color bars. Leave blank to use the current single-color bar fill.

color_values

colors used when group_colname is supplied. Named vectors are matched to group values; unnamed vectors follow group order and are extended with MOSuite colors when too few colors are supplied. Defaults to NULL; when NULL, mosuite_palette is used for data.frame dispatch and stored colors are used for multiOmicDataSet dispatch.

Value

ggplot barplot

See also

plot_read_depth() generic

Other plotters for multiOmicDataSets: plot_corr_heatmap,MOSuite::multiOmicDataSet-method, plot_histogram,MOSuite::multiOmicDataSet-method, plot_pca,MOSuite::multiOmicDataSet-method

Examples

# multiOmicDataSet
moo <- multiOmicDataSet(
  sample_metadata = nidap_sample_metadata,
  anno_dat = data.frame(),
  counts_lst = list(
    "raw" = nidap_raw_counts,
    "clean" = nidap_clean_raw_counts
  )
)

plot_read_depth(moo, count_type = "clean")