import os
import sys
sys.path.append(os.path.abspath("/users/amtseng/tfmodisco/src/"))
from tfmodisco.run_tfmodisco import import_shap_scores, import_tfmodisco_results
from motif.read_motifs import pfm_info_content, pfm_to_pwm, trim_motif_by_ic
from motif.match_motifs import match_motifs_to_database
from util import figure_to_vdom_image
import plot.viz_sequence as viz_sequence
import numpy as np
import h5py
import matplotlib.pyplot as plt
import vdom.helpers as vdomh
from IPython.display import display
# Define parameters/fetch arguments
tf_name = os.environ["TFM_TF_NAME"]
shap_scores_path = os.environ["TFM_SHAP_PATH"]
tfm_results_path = os.environ["TFM_TFM_PATH"]
hyp_score_key = os.environ["TFM_HYP_SCORE_KEY"]
if "TFM_MOTIF_CACHE" in os.environ:
tfm_motifs_cache_dir = os.environ["TFM_MOTIF_CACHE"]
else:
tfm_motifs_cache_dir = None
print("TF name: %s" % tf_name)
print("DeepSHAP scores path: %s" % shap_scores_path)
print("TF-MoDISco results path: %s" % tfm_results_path)
print("Importance score key: %s" % hyp_score_key)
print("Saved TF-MoDISco-derived motifs cache: %s" % tfm_motifs_cache_dir)
TF name: REST DeepSHAP scores path: /users/amtseng/tfmodisco/results/importance_scores/singletask_profile/REST_singletask_profile_fold8/task_6/REST_singletask_profile_task6_fold8_imp_scores.h5 TF-MoDISco results path: /users/amtseng/tfmodisco/results/tfmodisco/singletask_profile/REST_singletask_profile_fold8/task_6/REST_singletask_profile_task6_fold8_count_tfm.h5 Importance score key: count_hyp_scores Saved TF-MoDISco-derived motifs cache: /users/amtseng/tfmodisco/results/reports/tfmodisco_results//cache/singletask_profile/REST_singletask_profile_fold8/task_6/REST_singletask_profile_task6_fold8_count
# Define paths and constants
input_length = 2114
shap_score_center_size = 400
if tfm_motifs_cache_dir:
os.makedirs(tfm_motifs_cache_dir, exist_ok=True)
# Import SHAP coordinates and one-hot sequences
hyp_scores, _, one_hot_seqs, shap_coords = import_shap_scores(shap_scores_path, hyp_score_key, center_cut_size=shap_score_center_size)
# This cuts the sequences/scores off just as how TF-MoDISco saw them, but the coordinates are uncut
Importing SHAP scores: 100%|██████████| 12/12 [00:06<00:00, 1.92it/s]
# Import the TF-MoDISco results object
tfm_obj = import_tfmodisco_results(tfm_results_path, hyp_scores, one_hot_seqs, shap_score_center_size)
Plot the central region of some randomly selected actual importance scores
plot_slice = slice(int(shap_score_center_size / 4), int(3 * shap_score_center_size / 4))
for index in np.random.choice(hyp_scores.shape[0], size=5, replace=False):
viz_sequence.plot_weights((hyp_scores[index] * one_hot_seqs[index])[plot_slice], subticks_frequency=100)
motif_pfms, motif_hcwms, motif_cwms = [], [], [] # Save the trimmed PFMs, hCWMs, and CWMs
motif_pfms_short = [] # PFMs that are even more trimmed (for TOMTOM)
num_seqlets = [] # Number of seqlets for each motif
motif_seqlets = [] # Save seqlets of each motif
metaclusters = tfm_obj.metacluster_idx_to_submetacluster_results
num_metaclusters = len(metaclusters.keys())
if tfm_motifs_cache_dir:
motif_hdf5 = h5py.File(os.path.join(tfm_motifs_cache_dir, "all_motifs.h5"), "w")
for metacluster_i, metacluster_key in enumerate(metaclusters.keys()):
metacluster = metaclusters[metacluster_key]
display(vdomh.h3("Metacluster %d/%d" % (metacluster_i + 1, num_metaclusters)))
patterns = metacluster.seqlets_to_patterns_result.patterns
if not patterns:
break
motif_pfms.append([])
motif_hcwms.append([])
motif_cwms.append([])
motif_pfms_short.append([])
num_seqlets.append([])
motif_seqlets.append([])
num_patterns = len(patterns)
for pattern_i, pattern in enumerate(patterns):
seqlets = pattern.seqlets
display(vdomh.h4("Pattern %d/%d" % (pattern_i + 1, num_patterns)))
display(vdomh.p("%d seqlets" % len(seqlets)))
pfm = pattern["sequence"].fwd
hcwm = pattern["task0_hypothetical_contribs"].fwd
cwm = pattern["task0_contrib_scores"].fwd
pfm_fig = viz_sequence.plot_weights(pfm, subticks_frequency=10, return_fig=True)
hcwm_fig = viz_sequence.plot_weights(hcwm, subticks_frequency=10, return_fig=True)
cwm_fig = viz_sequence.plot_weights(cwm, subticks_frequency=10, return_fig=True)
pfm_fig.tight_layout()
hcwm_fig.tight_layout()
cwm_fig.tight_layout()
motif_table = vdomh.table(
vdomh.tr(
vdomh.td("Sequence (PFM)"),
vdomh.td(figure_to_vdom_image(pfm_fig))
),
vdomh.tr(
vdomh.td("Hypothetical contributions (hCWM)"),
vdomh.td(figure_to_vdom_image(hcwm_fig))
),
vdomh.tr(
vdomh.td("Actual contributions (CWM)"),
vdomh.td(figure_to_vdom_image(cwm_fig))
)
)
display(motif_table)
plt.close("all") # Remove all standing figures
# Trim motif based on information content
short_trimmed_pfm = trim_motif_by_ic(pfm, pfm)
motif_pfms_short[-1].append(short_trimmed_pfm)
# Expand trimming to +/- 4bp on either side
trimmed_pfm = trim_motif_by_ic(pfm, pfm, pad=4)
trimmed_hcwm = trim_motif_by_ic(pfm, hcwm, pad=4)
trimmed_cwm = trim_motif_by_ic(pfm, cwm, pad=4)
motif_pfms[-1].append(trimmed_pfm)
motif_hcwms[-1].append(trimmed_hcwm)
motif_cwms[-1].append(trimmed_cwm)
num_seqlets[-1].append(len(seqlets))
if tfm_motifs_cache_dir:
# Save results and figures
motif_id = "%d_%d" % (metacluster_i, pattern_i)
pfm_fig.savefig(os.path.join(tfm_motifs_cache_dir, motif_id + "_pfm_full.png"))
hcwm_fig.savefig(os.path.join(tfm_motifs_cache_dir, motif_id + "_hcwm_full.png"))
cwm_fig.savefig(os.path.join(tfm_motifs_cache_dir, motif_id + "_cwm_full.png"))
motif_dset = motif_hdf5.create_group(motif_id)
motif_dset.create_dataset("pfm_full", data=pfm, compression="gzip")
motif_dset.create_dataset("hcwm_full", data=hcwm, compression="gzip")
motif_dset.create_dataset("cwm_full", data=cwm, compression="gzip")
motif_dset.create_dataset("pfm_trimmed", data=trimmed_pfm, compression="gzip")
motif_dset.create_dataset("hcwm_trimmed", data=trimmed_hcwm, compression="gzip")
motif_dset.create_dataset("cwm_trimmed", data=trimmed_cwm, compression="gzip")
motif_dset.create_dataset("pfm_short_trimmed", data=short_trimmed_pfm, compression="gzip")
if tfm_motifs_cache_dir:
motif_hdf5.close()
2507 seqlets
Sequence (PFM) | |
Hypothetical contributions (hCWM) | |
Actual contributions (CWM) |
2281 seqlets
Sequence (PFM) | |
Hypothetical contributions (hCWM) | |
Actual contributions (CWM) |
2170 seqlets
Sequence (PFM) | |
Hypothetical contributions (hCWM) | |
Actual contributions (CWM) |
1699 seqlets
Sequence (PFM) | |
Hypothetical contributions (hCWM) | |
Actual contributions (CWM) |
906 seqlets
Sequence (PFM) | |
Hypothetical contributions (hCWM) | |
Actual contributions (CWM) |
316 seqlets
Sequence (PFM) | |
Hypothetical contributions (hCWM) | |
Actual contributions (CWM) |
247 seqlets
Sequence (PFM) | |
Hypothetical contributions (hCWM) | |
Actual contributions (CWM) |
81 seqlets
Sequence (PFM) | |
Hypothetical contributions (hCWM) | |
Actual contributions (CWM) |
55 seqlets
Sequence (PFM) | |
Hypothetical contributions (hCWM) | |
Actual contributions (CWM) |
44 seqlets
Sequence (PFM) | |
Hypothetical contributions (hCWM) | |
Actual contributions (CWM) |
42 seqlets
Sequence (PFM) | |
Hypothetical contributions (hCWM) | |
Actual contributions (CWM) |
37 seqlets
Sequence (PFM) | |
Hypothetical contributions (hCWM) | |
Actual contributions (CWM) |
38 seqlets
Sequence (PFM) | |
Hypothetical contributions (hCWM) | |
Actual contributions (CWM) |
35 seqlets
Sequence (PFM) | |
Hypothetical contributions (hCWM) | |
Actual contributions (CWM) |
30 seqlets
Sequence (PFM) | |
Hypothetical contributions (hCWM) | |
Actual contributions (CWM) |
30 seqlets
Sequence (PFM) | |
Hypothetical contributions (hCWM) | |
Actual contributions (CWM) |
Motifs are trimmed based on information content, and presented in descending order by number of supporting seqlets. The motifs are separated by metacluster. The motifs are presented as hCWMs. The forward orientation is defined as the orientation that is richer in purines.
colgroup = vdomh.colgroup(
vdomh.col(style={"width": "5%"}),
vdomh.col(style={"width": "5%"}),
vdomh.col(style={"width": "45%"}),
vdomh.col(style={"width": "45%"})
)
header = vdomh.thead(
vdomh.tr(
vdomh.th("#", style={"text-align": "center"}),
vdomh.th("Seqlets", style={"text-align": "center"}),
vdomh.th("Forward", style={"text-align": "center"}),
vdomh.th("Reverse", style={"text-align": "center"})
)
)
for i in range(len(motif_hcwms)):
display(vdomh.h3("Metacluster %d/%d" % (i + 1, num_metaclusters)))
body = []
for j in range(len(motif_hcwms[i])):
motif = motif_hcwms[i][j]
if np.sum(motif[:, [0, 2]]) > 0.5 * np.sum(motif):
# Forward is purine-rich, reverse-complement is pyrimidine-rich
f, rc = motif, np.flip(motif, axis=(0, 1))
else:
f, rc = np.flip(motif, axis=(0, 1)), motif
f_fig = viz_sequence.plot_weights(f, figsize=(20, 4), return_fig=True)
f_fig.tight_layout()
rc_fig = viz_sequence.plot_weights(rc, figsize=(20, 4), return_fig=True)
rc_fig.tight_layout()
if tfm_motifs_cache_dir:
# Save results and figures
motif_id = "%d_%d" % (i, j)
f_fig.savefig(os.path.join(tfm_motifs_cache_dir, motif_id + "_hcwm_trimmed_fwd.png"))
rc_fig.savefig(os.path.join(tfm_motifs_cache_dir, motif_id + "_hcwm_trimmed_rev.png"))
body.append(
vdomh.tr(
vdomh.td(str(j + 1)),
vdomh.td(str(num_seqlets[i][j])),
vdomh.td(figure_to_vdom_image(f_fig)),
vdomh.td(figure_to_vdom_image(rc_fig))
)
)
display(vdomh.table(colgroup, header, vdomh.tbody(*body)))
plt.close("all")
/users/amtseng/tfmodisco/src/plot/viz_sequence.py:152: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`). fig = plt.figure(figsize=figsize)
# | Seqlets | Forward | Reverse |
---|---|---|---|
1 | 2507 | ||
2 | 2281 | ||
3 | 2170 | ||
4 | 1699 | ||
5 | 906 | ||
6 | 316 | ||
7 | 247 | ||
8 | 81 | ||
9 | 55 | ||
10 | 44 | ||
11 | 42 | ||
12 | 37 |
# | Seqlets | Forward | Reverse |
---|---|---|---|
1 | 38 | ||
2 | 35 | ||
3 | 30 | ||
4 | 30 |
Here, the TF-MoDISco motifs are plotted as hCWMs, but the TOMTOM matches are shown as PWMs.
num_matches_to_keep = 10
num_matches_to_show = 5
header = vdomh.thead(
vdomh.tr(
vdomh.th("Motif ID", style={"text-align": "center"}),
vdomh.th("q-val", style={"text-align": "center"}),
vdomh.th("PWM", style={"text-align": "center"})
)
)
for i in range(len(motif_pfms)):
display(vdomh.h3("Metacluster %d/%d" % (i + 1, num_metaclusters)))
# Compute TOMTOM matches for all motifs in the metacluster at once
out_dir = os.path.join(tfm_motifs_cache_dir, "tomtom", "metacluster_%d" % i) if tfm_motifs_cache_dir else None
tomtom_matches = match_motifs_to_database(motif_pfms_short[i], top_k=num_matches_to_keep, temp_dir=out_dir)
for j in range(len(motif_pfms[i])):
display(vdomh.h4("Motif %d/%d" % (j + 1, len(motif_pfms[i]))))
viz_sequence.plot_weights(motif_hcwms[i][j])
body = []
for k, (match_name, match_pfm, match_qval) in enumerate(tomtom_matches[j]):
fig = viz_sequence.plot_weights(pfm_to_pwm(match_pfm), return_fig=True)
fig.tight_layout()
if k < num_matches_to_show:
body.append(
vdomh.tr(
vdomh.td(match_name),
vdomh.td(str(match_qval)),
vdomh.td(figure_to_vdom_image(fig))
)
)
if tfm_motifs_cache_dir:
# Save results and figures
motif_id = "%d_%d" % (i, j)
fig.savefig(os.path.join(out_dir, motif_id + ("_hit-%d.png" % (k + 1))))
else:
body.append(
vdomh.tr(
vdomh.td(match_name),
vdomh.td(str(match_qval)),
vdomh.td("Not shown")
)
)
if not body:
display(vdomh.p("No TOMTOM matches passing threshold"))
else:
display(vdomh.table(header, vdomh.tbody(*body)))
plt.close("all")
Motif ID | q-val | PWM |
---|---|---|
MA0138.2_REST | 0.09004889999999999 | |
REST_HUMAN.H11MO.0.A | 0.104098 |
Motif ID | q-val | PWM |
---|---|---|
MA0138.2_REST | 3.3948199999999993e-20 | |
REST_HUMAN.H11MO.0.A | 1.8220699999999997e-17 |
Motif ID | q-val | PWM |
---|---|---|
SPIB_HUMAN.H11MO.0.A | 1.07654e-14 | |
IRF4_HUMAN.H11MO.0.A | 3.54681e-13 | |
IRF8_HUMAN.H11MO.0.B | 2.5965e-12 | |
MA0081.2_SPIB | 7.94249e-12 | |
BC11A_HUMAN.H11MO.0.A | 2.39719e-11 | |
SPI1_HUMAN.H11MO.0.A | 3.62449e-11 | Not shown |
MA0080.5_SPI1 | 4.28069e-11 | Not shown |
MA0761.2_ETV1 | 0.000263909 | Not shown |
IRF1_HUMAN.H11MO.0.A | 0.000263909 | Not shown |
IRF2_HUMAN.H11MO.0.A | 0.000263909 | Not shown |
Motif ID | q-val | PWM |
---|---|---|
MA0138.2_REST | 4.47196e-12 | |
REST_HUMAN.H11MO.0.A | 1.08322e-10 |
Motif ID | q-val | PWM |
---|---|---|
REST_HUMAN.H11MO.0.A | 0.0042561000000000005 | |
MA0138.2_REST | 0.00518544 | |
TBX20_HUMAN.H11MO.0.D | 0.172767 |
No TOMTOM matches passing threshold
No TOMTOM matches passing threshold
No TOMTOM matches passing threshold
No TOMTOM matches passing threshold
Motif ID | q-val | PWM |
---|---|---|
MA0138.2_REST | 0.419152 |
Motif ID | q-val | PWM |
---|---|---|
MA1631.1_ASCL1(var.2) | 0.199855 | |
REST_HUMAN.H11MO.0.A | 0.199855 | |
MA0138.2_REST | 0.199855 | |
MA0139.1_CTCF | 0.199855 | |
CTCF_HUMAN.H11MO.0.A | 0.24868600000000002 | |
MA0830.2_TCF4 | 0.24868600000000002 | Not shown |
OSR2_HUMAN.H11MO.0.C | 0.278905 | Not shown |
Motif ID | q-val | PWM |
---|---|---|
TBX20_HUMAN.H11MO.0.D | 0.126616 | |
MAFA_HUMAN.H11MO.0.D | 0.420121 | |
ZSC16_HUMAN.H11MO.0.D | 0.420121 | |
MA0138.2_REST | 0.420121 |
Motif ID | q-val | PWM |
---|---|---|
USF2_HUMAN.H11MO.0.A | 0.0678102 | |
SP1_HUMAN.H11MO.0.A | 0.0678102 | |
AP2B_HUMAN.H11MO.0.B | 0.0678102 | |
MA1564.1_SP9 | 0.0678102 | |
MA1630.1_Znf281 | 0.0678102 | |
SP2_HUMAN.H11MO.0.A | 0.0678102 | Not shown |
MA0753.2_ZNF740 | 0.0678102 | Not shown |
SP3_HUMAN.H11MO.0.B | 0.0678102 | Not shown |
TBX15_HUMAN.H11MO.0.D | 0.0678102 | Not shown |
SP1_HUMAN.H11MO.1.A | 0.0678102 | Not shown |
No TOMTOM matches passing threshold
No TOMTOM matches passing threshold
No TOMTOM matches passing threshold