BPNet tf-Modisco report¶

url_dir = "http://mitra.stanford.edu/kundaje/avsec/chipnexus/oct-sox-nanog-klf/models/n_dil_layers=9/modisco/valid/plots/"
modisco_dir = "/users/avsec/workspace/basepair/data/processed/chipnexus/exp/models/oct-sox-nanog-klf/models/n_dil_layers=9/modisco/valid"

# Parameters
url_dir = "http://mitra.stanford.edu/kundaje/avsec/chipnexus/oct-sox-nanog-klf-dnase/models/n_dil_layers=9/modisco/valid/plots/"
modisco_dir = "."

from basepair.modisco import ModiscoResult
from basepair.config import get_data_dir
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from plotnine import *

/users/avsec/bin/anaconda3/envs/chipnexus/lib/python3.6/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
  from ._conv import register_converters as _register_converters
Using TensorFlow backend.
/users/avsec/bin/anaconda3/envs/chipnexus/lib/python3.6/site-packages/statsmodels/compat/pandas.py:56: FutureWarning: The pandas.core.datetools module is deprecated and will be removed in a future version. Please use the pandas.tseries module instead.
  from pandas.core import datetools

mr = ModiscoResult(f"{modisco_dir}/modisco.h5")
mr.open()

# Number of patterns
len(mr.patterns())

67

# Number of metaclusters
len(mr.metaclusters())

38

Number of seqlets per pattern¶

mc_stat = mr.metacluster_stats()

ggplot(aes(x="pattern", y='n'), mc_stat) + geom_bar(stat='identity') + \
    facet_wrap("~metacluster", ncol=4, labeller='label_both') + \
    ylab("Number of seqlets") + theme_classic()

<ggplot: (-9223363294391411526)>

Zoom-into the 500 seqlet range¶

ggplot(aes(x="pattern", y='n'), mc_stat) + geom_bar(stat='identity') + \
    facet_wrap("~metacluster", ncol=4, labeller='label_both') + \
    ylab("Number of seqlets") + theme_classic() + coord_cartesian(ylim=[0, 500])

<ggplot: (-9223363294597254484)>

Important tasks per metacluster¶

mcs_grouped = mc_stat.groupby("metacluster").n.agg(["count", "sum"]).reset_index()
fig, ax = plt.subplots(2, 1, sharex=False, figsize=(18,6), 
                       gridspec_kw={'height_ratios': [2,1]})
mcs_grouped.plot("metacluster", "count", 
                 label="# patterns per metacluster", style="o--", 
                 ax=ax[0], 
                 yticks=range(mcs_grouped['count'].max()+1),
                 xticks=range(38),
                 fontsize='large',
                 xlim=(-.5, len(mr.metaclusters()) - .5 ))
mcs_grouped.plot("metacluster", "sum", 
                 label="# seqlets per metacluster", 
                 style="o--", ax=ax[0], secondary_y=True)
ax[0].grid(linewidth=0.2)
mr.plot_metacluster_activity(ax[1], cbar=False)
ax[1].set_title("Importance score activity: Red = positive, Blue = negative");

mr.vdom(url_dir, is_open=True, trim_frac=0.08, letter_width=0.15, height=0.5)

Can not use cuDNN on context None: cannot compile with cuDNN. We got this error:
b'/tmp/try_flags_jt76n2se.c:4:19: fatal error: cudnn.h: No such file or directory\ncompilation terminated.\n'
Mapped name None to device cuda: TITAN X (Pascal) (0000:02:00.0)

print("Metaclusters heatmap")
import seaborn as sns
activity_patterns = np.array(mr.f.f['metaclustering_results']['attribute_vectors'])[
                    np.array(
        [x[0] for x in sorted(
                enumerate(mr.f.f['metaclustering_results']['metacluster_indices']),
               key=lambda x: x[1])])]
sns.heatmap(activity_patterns, center=0);

Metaclusters heatmap