Plot read depth as a bar plot

The first argument can be a multiOmicDataset object (moo) or a data.frame containing counts. For a moo, choose which counts slot to use with count_type & (optionally) sub_count_type.

Usage

plot_read_depth(moo_counts, ...)

Arguments

moo_counts

counts dataframe or multiOmicDataSet containing count_type & sub_count_type in the counts slot

...

arguments forwarded to method

Value

ggplot barplot

Methods

link to docs	class
plot_read_depth_moo	multiOmicDataSet
plot_read_depth_dat	data.frame

See also

Other plotters: plot_corr_heatmap(), plot_expr_heatmap(), plot_histogram(), plot_pca(), print_or_save_plot()

Other moo methods: batch_correct_counts(), clean_raw_counts(), diff_counts(), filter_counts(), filter_diff(), normalize_counts(), plot_corr_heatmap(), plot_expr_heatmap(), plot_histogram(), plot_pca(), run_deseq2(), set_color_pal()

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")


# dataframe
plot_read_depth(nidap_clean_raw_counts)