coalispr.bedgraph_analyze.info_plots

Module to plot info on program parameters or mapped data.

Attributes

logger

Functions

show_regions_vs_settings(tag, notitles[, logs10, thresh])

For picking some good settings, keeping enough regions but no too many.

show_mapped_vs_unmapped(tag, group, showdiscards, notitles)

Provide a quick impression of sequencing data.

Module Contents

coalispr.bedgraph_analyze.info_plots.logger
coalispr.bedgraph_analyze.info_plots.show_regions_vs_settings(tag, notitles, logs10=None, thresh=None)

For picking some good settings, keeping enough regions but no too many.

Parameters:

  • tag (str) – TAGCOLL or TAGUNCOLL

  • notitles (bool) – Flag to show figure title (default False, as legend will describe this).

  • logs10 (list) – List of possible values for UNSPECLOG10, including the configured UNSPECLOG10 to visualize the currently configured settings.

  • thresh (list) – List of possible values for LOG2BG, including the configured value.

Returns:

Plots showing effects of changing parameters on number of regions identified for 1. TAGUNCOLL and 2. TAGCOLL reads; can be saved as png or svg.

Return type:

Two diagrams with seaborn plots

coalispr.bedgraph_analyze.info_plots.show_mapped_vs_unmapped(tag, group, showdiscards, notitles, log2=False)

Provide a quick impression of sequencing data.

Parameters:

  • tag (str) – Label marking type of reads analyzed: TAGCOLL or TAGUNCOLL.

  • group (str) – Name determining grouping of samples, either CATEGORY, METHOD or FRACTION.

  • log2 (bool) – Use log2 scale if True.

Returns:

Plots showing total input numbers of mapped and unmapped (if available) reads; can be saved as png or svg.

Return type:

Diagrams with seaborn barh plots for collapsed or uncollapsed data;