coalispr.count_analyze.regioncount_plots

Module to plot count comparisons for a given region.

Relevant folders:

tsvpath/{REGI}_{READCOUNTS}_{TAGBAM}-bam/{REGI}_chrnam_nt1-nt2/

Attributes

logger
posslabels

Functions

plot_regioncounts(cntregion, countfram, group, strand, ...)	Compare counts for LIB, cDNA (COLLR) and associated
plot_regionlengths(cntregion, lengthframs, group, ...)	Obtain read-length distribution for a region in separate library samples.

Module Contents

coalispr.count_analyze.regioncount_plots.logger

coalispr.count_analyze.regioncount_plots.posslabels

coalispr.count_analyze.regioncount_plots.plot_regioncounts(cntregion, countfram, group, strand, notitles, log2, showdiscards)

Compare counts for LIB, cDNA (COLLR) and associated UNIQ and MULMAP reads for a region in given samples.

Relevant file-titles:

{LIBR | UNIQ | COLLR | UNIQ+COLLR}{COU}{_chrnam_nt1-nt2}TSV.

But not read from file; direct input as dataframe for processing.

label	a1_1	…	wt_2
library	3006.92	…	984.49
uniq	2990.0	…	820.0
cDNA	1868.74	…	632.32
uniqcDNA	1857.0	…	619.0
multimapperlibrary	49720.16	…	25251.54
multimappercDNA	1399.52	…	539.77

Parameters:

• cntregion (str) – String describing counted region, e.g. “6:56000-78900”.

• countfram (pd.DataFrame) – Dataframe with samples in columns and counts in rows with indices like “library”.

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

• strand (str) – Strand(s) with the counted reads.

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

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

• showdiscards (bool) – Show numbers for unused samples.

coalispr.count_analyze.regioncount_plots.plot_regionlengths(cntregion, lengthframs, group, readlen, strand, notitles, showdiscards)

Obtain read-length distribution for a region in separate library samples.

Relevant file-titles:

{LIBR | UNIQ | COLLR | UNIQ+COLLR}_[RLENCOUNTS}{_chrnam_nt1-nt2}TSV.

But not read from file; direct input as dict of dataframes for processing.

Parameters:

• cntregion (str) – String describing counted region, e.g. “6:56000-78900”.

• lengthframs (dict) – Dictionary of label: counter.get_lencount_frame()s with label in [ LIBR, UNIQ, COLLR, UNIQ+COLLR ] depending on calling function.

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

• readlen (tuple) – Limits for read lengths to include.

• strand (str) – Strand(s) with the counted reads.

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

• showdiscards (bool) – Show discarded samples.