coalispr.count_analyze.groupcompare_plots

Module to plot count comparisons between typed samples for a given group.

Relevant file names:

tsvpath/<countfolder>/{kind}_{RLENCOUNTS}_{strand}TSV

Attributes

logger

Functions

compare_5nt_lengths(rdkind, nt5, grp, grpdict, ...)

Compare read-length distribution for a given group of types and library

Module Contents

coalispr.count_analyze.groupcompare_plots.logger
coalispr.count_analyze.groupcompare_plots.compare_5nt_lengths(rdkind, nt5, grp, grpdict, samples, types, subtypes, readlen, var, strand, mulmap, use, notitles)

Compare read-length distribution for a given group of types and library samples for reads with a given start nt.

Relevant file-titles: {kind}_{RLENCOUNTS}_{strand}TSV.

Parameters:

  • rdkind (str) – One of LIBR, cDNAs (COLLR), CHRXTRA, possibly preceded by UNIQ or MULMAP to get only uniquely-mapped reads (UNIQ), or the repetitive sequences (MULMAP) like tRNA, rRNA or some transposons).

  • nt5 (str) – Start nucleotide; ‘T’, ‘A’, ‘G’, ‘C’ or ‘N’.

  • grp (str) – Original group (METHOD, FRACTION, CONDITION or GROUP), subgroups of which are in the comparison.

  • grpdict (dict) – Dictionary of subgroups vs samples in chosen group to compare.

  • samples (list) – List of short names for samples to use for plotting.

  • types (list) – List with names for grouping of samples, to compare.

  • subtypes (dict) – Collection of names for subgrouping of samples.

  • readlen (tuple) – Limits (int,int) of read lengths to show.

  • var (str) – Name for constant to select mean or median as standard for average; variance will be calculated.

  • strand (str) – One of COMBI, MUNR, or CORB.

  • mulmap (str) – Constant to refer to count files to be used, for UNIQ, MULMAP or none (‘’).

  • use (str) – Tag to filter particular reads.

  • notitles (bool) – Flag to set display of figure title on graph.