Plot TFBS in genome view

We will first plot the TFBS sites from ChIP-seq of GM12878 as loaded previously:

[1]:

import tfcomb
C = tfcomb.CombObj().from_pickle("../data/GM12878.pkl")

This object already contains TFBS to show:

[2]:

C.TFBS[:10]

[2]:

[chr4   11875   11876   ZBTB33  1000    .,
 chr4   116639  116640  JUNB    974     .,
 chr4   116678  116679  RUNX3   1000    .,
 chr4   121620  121621  RUNX3   1000    .,
 chr4   124050  124051  ZNF217  948     .,
 chr4   124052  124053  SMARCA5 802     .,
 chr4   124169  124170  NR2F1   634     .,
 chr4   124289  124290  CBX5    906     .,
 chr4   124363  124364  E4F1    1000    .,
 chr4   124365  124366  PKNOX1  1000    .]

Now, using .plot_TFBS, we can show the TFBS in a certain window:

[3]:

C.plot_TFBS(window_chrom = "chr4",
            window_start = 2441831,
            window_end = 2441885)

../_images/examples_plot_TFBS_genome_view_6_0.png

The function can also take fasta and bigwigs to show additional tracks below the TFBS:

[4]:

C.plot_TFBS(window_chrom = "chr4",
            window_start = 2441831,
            window_end = 2441885,
            fasta="../data/hg38_chr4.fa.gz",
            bigwigs = ["../data/GM12878_corrected.bw",
                       "../data/GM12878_footprints.bw"])

../_images/examples_plot_TFBS_genome_view_8_0.png

Plot TFBS from motifs

For TFBS with strand information, e.g. from motifs, .plot_TFBS will show the direction of the TFBS as arrows:

[5]:

C = tfcomb.CombObj(verbosity=0)
C.TFBS_from_motifs(regions="../data/GM12878_hg38_chr4_ATAC_peaks.bed",
                   motifs="../data/HOCOMOCOv11_HUMAN_motifs.txt",
                   genome="../data/hg38_chr4_masked.fa.gz",
                   threads=8)

[6]:

C.plot_TFBS(window_chrom = "chr4",
            window_start = 41709878,
            window_end = 41710236,
            bigwigs = ["../data/GM12878_corrected.bw",
                       "../data/GM12878_footprints.bw"])

../_images/examples_plot_TFBS_genome_view_12_0.png

Set figsize to control size of plot (the default is to estimate it from the number of tracks)

[7]:

C.plot_TFBS(window_chrom = "chr4",
            window_start = 41709878,
            window_end = 41710236,
            bigwigs = ["../data/GM12878_corrected.bw",
                       "../data/GM12878_footprints.bw"],
            figsize=(4,5))

../_images/examples_plot_TFBS_genome_view_14_0.png