swiss army heatmaps for delayed data frames and ChIPseq data
Project description
mbf_heatmap
Heatmaps for ChIPseq lanes and delayed DataFrames.
This is the swiss army knife of ChIPseq heatmaps.
Example usage:
from pathlib import Path
import mbf_align
import mbf_genomes
import mbf_genomics
import mbf_heatmap.chipseq as hc
import pypipegraph as ppg
ppg.new_pipegraph()
genome = mbf_genomes.EnsemblGenome('Homo_sapiens', 100)
lane1 = mbf_align.lanes.AlignedSample("one", "chipseq_one.bam", genome, False, None)
lane2 = mbf_align.lanes.AlignedSample("two", "chipseq_two.bam", genome, False, None)
input_regions = mbf_genomics.regions.Regions_FromBed("My_regions", "input.bed", genome)
hm = hc.Heatmap(
input_ergions,
[lane1, lane2],
region_strategy = hc.regions.RegionsFromCenter(2000) # +- 1000bp,
smoothing_strategy = hc.Smooth.SmoothExtendedReads(200) # extend reeads *by* 200bp
)
Path('results').mkdir(exists_ok=True)
hm.plot("results/my_first_heatmap.png",
norm = hc.norm.AsIs(),
order = hc.order.AsIs(),
)
Part of the mbf_* suite from https://github.com/IMTMarburg
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