TF-MoDISco results

Summary of motifs

TOMTOM matches to motifs

Sample of seqlets for each motif

In [1]:
import os
import util
from tomtom import match_motifs_to_database
import viz_sequence
import numpy as np
import pandas as pd
import sklearn.cluster
import scipy.cluster.hierarchy
import matplotlib.pyplot as plt
import matplotlib.font_manager as font_manager
import vdom.helpers as vdomh
from IPython.display import display
import tqdm
tqdm.tqdm_notebook()

/users/amtseng/miniconda3/envs/tfmodisco-mini/lib/python3.7/site-packages/ipykernel_launcher.py:14: TqdmDeprecationWarning: This function will be removed in tqdm==5.0.0
Please use `tqdm.notebook.tqdm` instead of `tqdm.tqdm_notebook`
Out[1]:
0it [00:00, ?it/s]
In [2]:
# Plotting defaults
font_manager.fontManager.ttflist.extend(
    font_manager.createFontList(
        font_manager.findSystemFonts(fontpaths="/users/amtseng/modules/fonts")
    )
)
plot_params = {
    "figure.titlesize": 22,
    "axes.titlesize": 22,
    "axes.labelsize": 20,
    "legend.fontsize": 18,
    "xtick.labelsize": 16,
    "ytick.labelsize": 16,
    "font.family": "Roboto",
    "font.weight": "bold"
}
plt.rcParams.update(plot_params)

/users/amtseng/miniconda3/envs/tfmodisco-mini/lib/python3.7/site-packages/ipykernel_launcher.py:4: MatplotlibDeprecationWarning: 
The createFontList function was deprecated in Matplotlib 3.2 and will be removed two minor releases later. Use FontManager.addfont instead.
  after removing the cwd from sys.path.

Define constants and paths

In [3]:
# Define parameters/fetch arguments
preds_path = os.environ["TFM_PRED_PATH"]
shap_scores_path = os.environ["TFM_SHAP_PATH"]
tfm_results_path = os.environ["TFM_TFM_PATH"]
peak_bed_paths = [os.environ["TFM_PEAKS_PATH"]]

print("Predictions path: %s" % preds_path)
print("DeepSHAP scores path: %s" % shap_scores_path)
print("TF-MoDISco results path: %s" % tfm_results_path)
print("Peaks path: %s" % peak_bed_paths[0])

Predictions path: /users/zahoor/TF-Atlas/02-16-2021/predictions/ENCSR000EFS/profile_predictions.h5
DeepSHAP scores path: /users/zahoor/TF-Atlas/02-16-2021/shap/ENCSR000EFS/profile_scores_alex_format.h5
TF-MoDISco results path: /users/zahoor/TF-Atlas/02-16-2021/modisco/ENCSR000EFS/profile/modisco_results.hd5
Peaks path: /users/zahoor/TF-Atlas/data/idr_peaks//ENCFF190CGV.bed.gz
In [4]:
# Define constants
input_length, profile_length = 2114, 1000
shap_score_center_size = 400
profile_display_center_size = 400
hyp_score_key = "hyp_scores"
task_index = None

Helper functions

In [5]:
def extract_profiles_and_coords(
    seqlets_arr, one_hot_seqs, hyp_scores, true_profs, pred_profs, pred_coords,
    input_length, profile_length, input_center_cut_size, profile_center_cut_size,
    task_index=None
):
    """
    From the seqlets object of a TF-MoDISco pattern's seqlets and alignments,
    extracts the predicted and observed profiles of the model, as well as the
    set of coordinates for the seqlets.
    Arguments:
        `seqlets_arr`: a TF-MoDISco pattern's seqlets object array (N-array)
        `one_hot_seqs`: an N x R x 4 array of input sequences, where R is
            the cut centered size
        `hyp_scores`: an N x R x 4 array of hypothetical importance scores
        `true_profs`: an N x T x O x 2 array of true profile counts
        `pred_profs`: an N x T x O x 2 array of predicted profile probabilities
        `pred_coords`: an N x 3 object array of coordinates for the input sequence
            underlying the predictions
        `input_length`: length of original input sequences, I
        `profile_length`: length of profile predictions, O
        `input_center_cut_size`: centered cut size of SHAP scores used
        `profile_center_cut_size`: size to cut profiles to when returning them, P
        `task_index`: index of task to focus on for profiles; if None, returns
            profiles for all tasks
    Returns an N x (T or 1) x P x 2 array of true profile counts, an
    N x (T or 1) x P x 2 array of predicted profile probabilities, an N x Q x 4
    array of one-hot seqlet sequences, an N x Q x 4 array of hypothetical seqlet
    importance scores, and an N x 3 object array of seqlet coordinates, where P
    is the profile cut size and Q is the seqlet length. Returned profiles are
    centered at the same center as the seqlets.
    Note that it is important that the seqlet indices match exactly with the indices
    out of the N. This should be the exact sequences in the original SHAP scores.
    """
    true_seqlet_profs, pred_seqlet_profs, seqlet_seqs, seqlet_hyps, seqlet_coords = [], [], [], [], []
    
    def seqlet_coord_to_profile_coord(seqlet_coord):
        return seqlet_coord + ((input_length - input_center_cut_size) // 2) - ((input_length - profile_length) // 2)
    
    def seqlet_coord_to_input_coord(seqlet_coord):
        return seqlet_coord + ((input_length - input_center_cut_size) // 2)
        
    # For each seqlet, fetch the true/predicted profiles
    for seqlet in seqlets_arr:
        coord_index = seqlet.coor.example_idx
        seqlet_start = seqlet.coor.start
        seqlet_end = seqlet.coor.end
        seqlet_rc = seqlet.coor.is_revcomp
        
        # Get indices of profile to cut out
        seqlet_center = (seqlet_start + seqlet_end) // 2
        prof_center = seqlet_coord_to_profile_coord(seqlet_center)
        prof_start = prof_center - (profile_center_cut_size // 2)
        prof_end = prof_start + profile_center_cut_size
        
        if task_index is None or true_profs.shape[1] == 1:
            # Use all tasks if the predictions only have 1 task to begin with
            task_start, task_end = None, None
        else:
            task_start, task_end = task_index, task_index + 1
            
        true_prof = true_profs[coord_index, task_start:task_end, prof_start:prof_end]  # (T or 1) x P x 2
        pred_prof = pred_profs[coord_index, task_start:task_end, prof_start:prof_end]  # (T or 1) x P x 2
        
        true_seqlet_profs.append(true_prof)
        pred_seqlet_profs.append(pred_prof)
        
        # The one-hot-sequences and hypothetical scores are assumed to already by cut/centered,
        # so the indices match the seqlet indices
        if seqlet_rc:
            seqlet_seqs.append(np.flip(one_hot_seqs[coord_index, seqlet_start:seqlet_end], axis=(0, 1)))
            seqlet_hyps.append(np.flip(hyp_scores[coord_index, seqlet_start:seqlet_end], axis=(0, 1)))
        else:
            seqlet_seqs.append(one_hot_seqs[coord_index, seqlet_start:seqlet_end])
            seqlet_hyps.append(hyp_scores[coord_index, seqlet_start:seqlet_end])
            
        # Get the coordinates of the seqlet based on the input coordinates
        inp_start = seqlet_coord_to_input_coord(seqlet_start)
        inp_end = seqlet_coord_to_input_coord(seqlet_end)
        chrom, start, _ = pred_coords[coord_index]
        seqlet_coords.append([chrom, start + inp_start, start + inp_end])
    
    return np.stack(true_seqlet_profs), np.stack(pred_seqlet_profs), np.stack(seqlet_seqs), np.stack(seqlet_hyps), np.array(seqlet_coords, dtype=object)
In [6]:
def plot_profiles(seqlet_true_profs, seqlet_pred_profs, kmeans_clusters=5):
    """
    Plots the given profiles with a heatmap.
    Arguments:
        `seqlet_true_profs`: an N x O x 2 NumPy array of true profiles, either as raw
            counts or probabilities (they will be normalized)
        `seqlet_pred_profs`: an N x O x 2 NumPy array of predicted profiles, either as
            raw counts or probabilities (they will be normalized)
        `kmeans_cluster`: when displaying profile heatmaps, there will be this
            many clusters
    """
    assert len(seqlet_true_profs.shape) == 3
    assert seqlet_true_profs.shape == seqlet_pred_profs.shape
    num_profs, width, _ = seqlet_true_profs.shape

    # First, normalize the profiles along the output profile dimension
    def normalize(arr, axis=0):
        arr_sum = np.sum(arr, axis=axis, keepdims=True)
        arr_sum[arr_sum == 0] = 1  # If 0, keep 0 as the quotient instead of dividing by 0
        return arr / arr_sum
    true_profs_norm = normalize(seqlet_true_profs, axis=1)
    pred_profs_norm = normalize(seqlet_pred_profs, axis=1)

    # Compute the mean profiles across all examples
    true_profs_mean = np.mean(true_profs_norm, axis=0)
    pred_profs_mean = np.mean(pred_profs_norm, axis=0)

    # Perform k-means clustering on the predicted profiles, with the strands pooled
    kmeans_clusters = max(5, num_profs // 50)  # Set number of clusters based on number of profiles, with minimum
    kmeans = sklearn.cluster.KMeans(n_clusters=kmeans_clusters)
    cluster_assignments = kmeans.fit_predict(
        np.reshape(pred_profs_norm, (pred_profs_norm.shape[0], -1))
    )

    # Perform hierarchical clustering on the cluster centers to determine optimal ordering
    kmeans_centers = kmeans.cluster_centers_
    cluster_order = scipy.cluster.hierarchy.leaves_list(
        scipy.cluster.hierarchy.optimal_leaf_ordering(
            scipy.cluster.hierarchy.linkage(kmeans_centers, method="centroid"), kmeans_centers
        )
    )

    # Order the profiles so that the cluster assignments follow the optimal ordering
    cluster_inds = []
    for cluster_id in cluster_order:
        cluster_inds.append(np.where(cluster_assignments == cluster_id)[0])
    cluster_inds = np.concatenate(cluster_inds)

    # Compute a matrix of profiles, normalized to the maximum height, ordered by clusters
    def make_profile_matrix(flat_profs, order_inds):
        matrix = flat_profs[order_inds]
        maxes = np.max(matrix, axis=1, keepdims=True)
        maxes[maxes == 0] = 1  # If 0, keep 0 as the quotient instead of dividing by 0
        return matrix / maxes
    true_matrix = make_profile_matrix(true_profs_norm, cluster_inds)
    pred_matrix = make_profile_matrix(pred_profs_norm, cluster_inds)

    # Create a figure with the right dimensions
    mean_height = 4
    heatmap_height = min(num_profs * 0.004, 8)
    fig_height = mean_height + (2 * heatmap_height)
    fig, ax = plt.subplots(
        3, 2, figsize=(16, fig_height), sharex=True,
        gridspec_kw={
            "width_ratios": [1, 1],
            "height_ratios": [mean_height / fig_height, heatmap_height / fig_height, heatmap_height / fig_height]
        }
    )

    # Plot the average predictions
    ax[0, 0].plot(true_profs_mean[:, 0], color="darkslateblue")
    ax[0, 0].plot(-true_profs_mean[:, 1], color="darkorange")
    ax[0, 1].plot(pred_profs_mean[:, 0], color="darkslateblue")
    ax[0, 1].plot(-pred_profs_mean[:, 1], color="darkorange")

    # Set axes on average predictions
    max_mean_val = max(np.max(true_profs_mean), np.max(pred_profs_mean))
    mean_ylim = max_mean_val * 1.05  # Make 5% higher
    ax[0, 0].set_title("True profiles")
    ax[0, 0].set_ylabel("Average probability")
    ax[0, 1].set_title("Predicted profiles")
    for j in (0, 1):
        ax[0, j].set_ylim(-mean_ylim, mean_ylim)
        ax[0, j].label_outer()

    # Plot the heatmaps
    ax[1, 0].imshow(true_matrix[:, :, 0], interpolation="nearest", aspect="auto", cmap="Blues")
    ax[1, 1].imshow(pred_matrix[:, :, 0], interpolation="nearest", aspect="auto", cmap="Blues")
    ax[2, 0].imshow(true_matrix[:, :, 1], interpolation="nearest", aspect="auto", cmap="Oranges")
    ax[2, 1].imshow(pred_matrix[:, :, 1], interpolation="nearest", aspect="auto", cmap="Oranges")

    # Set axes on heatmaps
    for i in (1, 2):
        for j in (0, 1):
            ax[i, j].set_yticks([])
            ax[i, j].set_yticklabels([])
            ax[i, j].label_outer()
    width = true_matrix.shape[1]
    delta = 100
    num_deltas = (width // 2) // delta
    labels = list(range(max(-width // 2, -num_deltas * delta), min(width // 2, num_deltas * delta) + 1, delta))
    tick_locs = [label + max(width // 2, num_deltas * delta) for label in labels]
    for j in (0, 1):
        ax[2, j].set_xticks(tick_locs)
        ax[2, j].set_xticklabels(labels)
        ax[2, j].set_xlabel("Distance from peak summit (bp)")

    fig.tight_layout()
    plt.show()
In [7]:
def get_summit_distances(coords, peak_table):
    """
    Given a set of coordinates, computes the distance of the center of each
    coordinate to the nearest summit.
    Arguments:
        `coords`: an N x 3 object array of coordinates
        `peak_table`: a 6-column table of peak data, as imported by
            `import_peak_table`
    Returns and N-array of integers, which is the distance of each coordinate
    midpoint to the nearest coordinate.
    """
    chroms = coords[:, 0]
    midpoints = (coords[:, 1] + coords[:, 2]) // 2
    dists = []
    for i in range(len(coords)):
        chrom = chroms[i]
        midpoint = midpoints[i]
        rows = peak_table[peak_table["chrom"] == chrom]
        dist_arr = (midpoint - rows["summit"]).values
        min_dist = dist_arr[np.argmin(np.abs(dist_arr))]
        dists.append(min_dist)
    return np.array(dists)
In [8]:
def plot_summit_dists(summit_dists):
    """
    Plots the distribution of seqlet distances to summits.
    Arguments:
        `summit_dists`: the array of distances as returned by
            `get_summit_distances`
    """
    plt.figure(figsize=(8, 6))
    num_bins = max(len(summit_dists) // 30, 20)
    plt.hist(summit_dists, bins=num_bins, color="purple")
    plt.title("Histogram of distance of seqlets to peak summits")
    plt.xlabel("Signed distance from seqlet center to nearest peak summit (bp)")
    plt.show()

Import SHAP scores, profile predictions, and TF-MoDISco results

In [9]:
# Import SHAP coordinates and one-hot sequences
hyp_scores, _, one_hot_seqs, shap_coords = util.import_shap_scores(shap_scores_path, hyp_score_key, center_cut_size=shap_score_center_size, remove_non_acgt=False)
# This cuts the sequences/scores off just as how TF-MoDISco saw them, but the coordinates are uncut

Importing SHAP scores: 100%|██████████| 22/22 [00:08<00:00,  2.74it/s]
In [10]:
# Import the set of all profiles and their coordinates
true_profs, pred_profs, all_pred_coords = util.import_profiles(preds_path)



















In [11]:



    


# Import the set of peaks
peak_table = util.import_peak_table(peak_bed_paths)



    













In [12]:



    


# Subset the predicted profiles/coordinates to the task-specific SHAP coordinates/scores
shap_coords_table = pd.DataFrame(shap_coords, columns=["chrom", "start", "end"])
pred_coords_table = pd.DataFrame(all_pred_coords, columns=["chrom", "start", "end"])

subset_inds = pred_coords_table.reset_index().drop_duplicates(["chrom", "start", "end"]).merge(
    shap_coords_table.reset_index(), on=["chrom", "start", "end"]
).sort_values("index_y")["index_x"].values

true_profs = true_profs[subset_inds]
pred_profs = pred_profs[subset_inds]
pred_coords = all_pred_coords[subset_inds]

# Make sure the coordinates all match
assert np.all(pred_coords == shap_coords)



    













In [13]:



    


# Import the TF-MoDISco results object
tfm_obj = util.import_tfmodisco_results(tfm_results_path, hyp_scores, one_hot_seqs, shap_score_center_size)



    















Plot some SHAP score tracks
Plot the central region of some randomly selected actual importance scores













In [14]:



    


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])[100:300], subticks_frequency=100)



    















    

















    

















    

















    

















    






























Plot TF-MoDISco results
Plot all motifs by metacluster













In [15]:



    


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())
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(util.figure_to_vdom_image(pfm_fig))
            ),
            vdomh.tr(
                vdomh.td("Hypothetical contributions (hCWM)"),
                vdomh.td(util.figure_to_vdom_image(hcwm_fig))
            ),
            vdomh.tr(
                vdomh.td("Actual contributions (CWM)"),
                vdomh.td(util.figure_to_vdom_image(cwm_fig))
            )
        )
        display(motif_table)
        plt.close("all")  # Remove all standing figures
        
        # Trim motif based on total contribution
        score = np.sum(np.abs(cwm), axis=1)
        trim_thresh = np.max(score) * 0.2  # Cut off anything less than 20% of max score
        pass_inds = np.where(score >= trim_thresh)[0]
        
        short_trimmed_pfm = pfm[np.min(pass_inds): np.max(pass_inds) + 1]
        motif_pfms_short[-1].append(short_trimmed_pfm)
        
        # Expand trimming to +/- 4bp on either side
        start, end = max(0, np.min(pass_inds) - 4), min(len(cwm), np.max(pass_inds) + 4 + 1)
        trimmed_pfm = pfm[start:end]
        trimmed_hcwm = hcwm[start:end]
        trimmed_cwm = cwm[start:end]
        
        motif_pfms[-1].append(trimmed_pfm)
        motif_hcwms[-1].append(trimmed_hcwm)
        motif_cwms[-1].append(trimmed_cwm)
        
        num_seqlets[-1].append(len(seqlets))
        
        seqlet_true_profs, seqlet_pred_profs, seqlet_seqs, seqlet_hyps, seqlet_coords = extract_profiles_and_coords(
            seqlets, one_hot_seqs, hyp_scores, true_profs, pred_profs, pred_coords,
            input_length, profile_length, shap_score_center_size,
            profile_display_center_size, task_index=task_index
        )
        
        motif_seqlets[-1].append((seqlet_seqs, seqlet_hyps))

        assert np.allclose(np.sum(seqlet_seqs, axis=0) / len(seqlet_seqs), pattern["sequence"].fwd)
        # ^Sanity check: PFM derived from seqlets match the PFM stored in the pattern
        plot_profiles(
            # Flatten to NT x O x 2
            np.reshape(seqlet_true_profs, (-1, seqlet_true_profs.shape[2], seqlet_true_profs.shape[3])),
            np.reshape(seqlet_pred_profs, (-1, seqlet_pred_profs.shape[2], seqlet_pred_profs.shape[3]))
        )
        
        summit_dists = get_summit_distances(seqlet_coords, peak_table)
        plot_summit_dists(summit_dists)



    















    







Metacluster 1/2










    







Pattern 1/10










    







5080 seqlets










    







Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)










    

















    

















    







Pattern 2/10










    







2097 seqlets










    







Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)










    

















    

















    







Pattern 3/10










    







1655 seqlets










    







Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)










    

















    

















    







Pattern 4/10










    







882 seqlets










    







Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)










    

















    

















    







Pattern 5/10










    







874 seqlets










    







Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)










    

















    

















    







Pattern 6/10










    







860 seqlets










    







Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)










    

















    

















    







Pattern 7/10










    







828 seqlets










    







Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)










    

















    

















    







Pattern 8/10










    







360 seqlets










    







Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)










    

















    

















    







Pattern 9/10










    







69 seqlets










    







Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)










    

















    

















    







Pattern 10/10










    







47 seqlets










    







Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)










    

















    

















    







Metacluster 2/2










    







Pattern 1/2










    







59 seqlets










    







Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)










    

















    

















    







Pattern 2/2










    







138 seqlets










    







Sequence (PFM)
Hypothetical contributions (hCWM)
Actual contributions (CWM)










    

















    






























Summary of motifs
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.













In [16]:



    


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()

        body.append(
            vdomh.tr(
                vdomh.td(str(j + 1)),
                vdomh.td(str(num_seqlets[i][j])),
                vdomh.td(util.figure_to_vdom_image(f_fig)),
                vdomh.td(util.figure_to_vdom_image(rc_fig))
            )
        )
    display(vdomh.table(colgroup, header, vdomh.tbody(*body)))
    plt.close("all")



    















    







Metacluster 1/2










    







#SeqletsForwardReverse
15080
22097
31655
4882
5874
6860
7828
8360
969
1047










    







Metacluster 2/2










    







#SeqletsForwardReverse
159
2138























Top TOMTOM matches for each motif
Here, the TF-MoDISco motifs are plotted as hCWMs, but the TOMTOM matches are shown as PWMs.













In [17]:



    


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
    tomtom_matches = match_motifs_to_database(motif_pfms_short[i], top_k=num_matches_to_keep)
    
    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(util.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(util.figure_to_vdom_image(fig))
                    )
                )
            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")



    















    







Metacluster 1/2










    







Motif 1/10










    

















    







Motif IDq-valPWM
JUN_HUMAN.H11MO.0.A1.10792e-07
FOSL2_HUMAN.H11MO.0.A1.10792e-07
MA0099.3_FOS::JUN1.64465e-06
MA1622.1_Smad2::Smad31.64465e-06
FOSB_HUMAN.H11MO.0.A1.64465e-06
MA1130.1_FOSL2::JUN2.29266e-06Not shown
MA1141.1_FOS::JUND2.29266e-06Not shown
MA1128.1_FOSL1::JUN2.29266e-06Not shown
FOSL1_HUMAN.H11MO.0.A3.6547699999999997e-06Not shown
JUND_HUMAN.H11MO.0.A4.8589400000000004e-06Not shown










    







Motif 2/10










    

















    







Motif IDq-valPWM
MA0605.2_ATF33.07286e-08
MA1127.1_FOSB::JUN2.76251e-07
MA1131.1_FOSL2::JUN(var.2)5.6916e-07
JDP2_HUMAN.H11MO.0.D5.6916e-07
MA1140.2_JUNB(var.2)6.75297e-07
MA1145.1_FOSL2::JUND(var.2)8.42535e-07Not shown
MA0656.1_JDP2(var.2)8.42535e-07Not shown
MA1139.1_FOSL2::JUNB(var.2)9.84808e-07Not shown
ATF7_HUMAN.H11MO.0.D1.2334000000000001e-06Not shown
CREB5_HUMAN.H11MO.0.D1.2334000000000001e-06Not shown










    







Motif 3/10










    

















    







Motif IDq-valPWM
TAL1_HUMAN.H11MO.0.A9.192169999999999e-10
GATA2_HUMAN.H11MO.0.A4.20171e-09
GATA1_HUMAN.H11MO.0.A2.2657699999999998e-07
GATA4_HUMAN.H11MO.0.A8.61989e-05
GATA1_HUMAN.H11MO.1.A0.00237038
GATA2_HUMAN.H11MO.1.A0.00237038Not shown
MA0036.3_GATA20.00898687Not shown
MA0140.2_GATA1::TAL10.00898687Not shown
GATA3_HUMAN.H11MO.0.A0.017591700000000002Not shown
MYOG_HUMAN.H11MO.0.B0.0249684Not shown










    







Motif 4/10










    

















    







Motif IDq-valPWM
ATF4_HUMAN.H11MO.0.A6.046430000000001e-09
CEBPG_HUMAN.H11MO.0.B1.02601e-05
MA0833.2_ATF40.000116001
DDIT3_HUMAN.H11MO.0.D0.00023155700000000002
MA1636.1_CEBPG(var.2)0.000648453
BATF_HUMAN.H11MO.1.A0.000671029Not shown
CEBPD_HUMAN.H11MO.0.C0.00699875Not shown
NFIL3_HUMAN.H11MO.0.D0.010268000000000001Not shown
MA0488.1_JUN0.010268000000000001Not shown
CEBPB_HUMAN.H11MO.0.A0.0114714Not shown










    







Motif 5/10










    

















    







Motif IDq-valPWM
MA0488.1_JUN0.000790127
MA0656.1_JDP2(var.2)0.000790127
MA0492.1_JUND(var.2)0.000790127
MA0605.2_ATF30.000790127
MA1140.2_JUNB(var.2)0.000790127
MA1139.1_FOSL2::JUNB(var.2)0.0008532069999999999Not shown
ATF2_HUMAN.H11MO.0.B0.0008871630000000001Not shown
MA1475.1_CREB3L4(var.2)0.0008871630000000001Not shown
ATF2_HUMAN.H11MO.1.B0.0008871630000000001Not shown
MA0840.1_Creb50.00109473Not shown










    







Motif 6/10










    

















    







Motif IDq-valPWM
USF2_HUMAN.H11MO.0.A3.22282e-07
SP2_HUMAN.H11MO.0.A6.65974e-05
MXI1_HUMAN.H11MO.0.A6.65974e-05
MA0104.4_MYCN0.00020155900000000003
SP1_HUMAN.H11MO.0.A0.000212175
USF1_HUMAN.H11MO.0.A0.000746571Not shown
SP3_HUMAN.H11MO.0.B0.000815313Not shown
MA0004.1_Arnt0.00227642Not shown
MA0692.1_TFEB0.00227642Not shown
MA0636.1_BHLHE410.00227642Not shown










    







Motif 7/10










    

















    







Motif IDq-valPWM
CTCF_HUMAN.H11MO.0.A3.02343e-14
MA0139.1_CTCF1.87323e-11
CTCFL_HUMAN.H11MO.0.A8.96927e-09
MA1102.2_CTCFL1.2226700000000001e-05
ZIC3_HUMAN.H11MO.0.B0.167054
SNAI1_HUMAN.H11MO.0.C0.167054Not shown
MA1568.1_TCF21(var.2)0.167054Not shown
KLF8_HUMAN.H11MO.0.C0.167054Not shown
MA0155.1_INSM10.167054Not shown
MA1638.1_HAND20.167054Not shown










    







Motif 8/10










    

















    







Motif IDq-valPWM
GABPA_HUMAN.H11MO.0.A1.54538e-07
ELK1_HUMAN.H11MO.0.B8.51394e-06
ELF2_HUMAN.H11MO.0.C1.1239300000000001e-05
MA0765.2_ETV51.1239300000000001e-05
MA0076.2_ELK41.21898e-05
SP2_HUMAN.H11MO.0.A1.32807e-05Not shown
SP1_HUMAN.H11MO.0.A1.50478e-05Not shown
MA0598.3_EHF7.44003e-05Not shown
MA0763.1_ETV38.773459999999998e-05Not shown
MA0760.1_ERF8.773459999999998e-05Not shown










    







Motif 9/10










    

















    







Motif IDq-valPWM
FOSB_HUMAN.H11MO.0.A4.97333e-05
MA0655.1_JDP20.000171441
JUN_HUMAN.H11MO.0.A0.000286918
FOS_HUMAN.H11MO.0.A0.000286918
MA1144.1_FOSL2::JUND0.000286918
MA1138.1_FOSL2::JUNB0.000286918Not shown
MA1142.1_FOSL1::JUND0.000286918Not shown
MA0478.1_FOSL20.000297199Not shown
MA1130.1_FOSL2::JUN0.000297199Not shown
JUND_HUMAN.H11MO.0.A0.000297199Not shown










    







Motif 10/10










    

















    







Motif IDq-valPWM
MA1142.1_FOSL1::JUND0.0187191
MA0655.1_JDP20.0187191
FOSB_HUMAN.H11MO.0.A0.0187191
MA1135.1_FOSB::JUNB0.0187191
MA1138.1_FOSL2::JUNB0.0187191
MA0478.1_FOSL20.0187191Not shown
MA0099.3_FOS::JUN0.0187191Not shown
MA1144.1_FOSL2::JUND0.0187191Not shown
FOS_HUMAN.H11MO.0.A0.0187191Not shown
MA1132.1_JUN::JUNB0.0195691Not shown










    







Metacluster 2/2










    







Motif 1/2










    

















    







Motif IDq-valPWM
SP2_HUMAN.H11MO.0.A0.0019145
SP3_HUMAN.H11MO.0.B0.00948304
SP1_HUMAN.H11MO.0.A0.0420202
MA1522.1_MAZ0.0420202
ZFX_HUMAN.H11MO.1.A0.0510388
AP2B_HUMAN.H11MO.0.B0.0510388Not shown
KLF3_HUMAN.H11MO.0.B0.07809479999999999Not shown
MA1615.1_Plagl10.07809479999999999Not shown
KLF6_HUMAN.H11MO.0.A0.07809479999999999Not shown
PLAL1_HUMAN.H11MO.0.D0.07809479999999999Not shown










    







Motif 2/2










    

















    







Motif IDq-valPWM
TBX15_HUMAN.H11MO.0.D8.572850000000001e-08
SP2_HUMAN.H11MO.0.A9.63176e-08
SP3_HUMAN.H11MO.0.B2.0241599999999998e-07
KLF16_HUMAN.H11MO.0.D2.37958e-07
SP1_HUMAN.H11MO.0.A4.6848199999999997e-07
MAZ_HUMAN.H11MO.0.A5.77768e-07Not shown
ZN467_HUMAN.H11MO.0.C1.0650399999999998e-06Not shown
WT1_HUMAN.H11MO.0.C2.9994400000000003e-06Not shown
PATZ1_HUMAN.H11MO.0.C2.9994400000000003e-06Not shown
VEZF1_HUMAN.H11MO.0.C3.6328800000000003e-06Not shown























Sample of seqlets supporting each motif
Here, the motifs are presented as hCWMs, along with the actual importance scores of a random sample of seqlets that support the motif.













In [18]:



    


num_seqlets_to_show = 10

colgroup = vdomh.colgroup(
    vdomh.col(style={"width": "50%"}),
    vdomh.col(style={"width": "50%"})
)

header = vdomh.thead(
    vdomh.tr(
        vdomh.th("Motif hCWM", style={"text-align": "center"}),
        vdomh.th("Seqlets", style={"text-align": "center"})
    )
)

for i in range(len(motif_hcwms)):
    display(vdomh.h3("Metacluster %d/%d" % (i + 1, num_metaclusters)))
    
    for j in range(len(motif_hcwms[i])):
        display(vdomh.h4("Motif %d/%d" % (j + 1, len(motif_hcwms[i]))))
        
        motif_fig = viz_sequence.plot_weights(motif_hcwms[i][j], figsize=(20, 4), return_fig=True)
        motif_fig.tight_layout()
        
        seqlet_seqs, seqlet_hyps = motif_seqlets[i][j]
        
        sample_size = min(num_seqlets_to_show, len(seqlet_seqs))
        sample_inds = np.random.choice(len(seqlet_seqs), size=sample_size, replace=False)
        sample = []
        for k in sample_inds:
            fig = viz_sequence.plot_weights(seqlet_hyps[k] * seqlet_seqs[k], subticks_frequency=10, return_fig=True)
            fig.tight_layout()
            sample.append(util.figure_to_vdom_image(fig))
        body = vdomh.tbody(vdomh.tr(vdomh.td(util.figure_to_vdom_image(motif_fig)), vdomh.td(*sample)))
        display(vdomh.table(colgroup, header, body))
        plt.close("all")



    















    







Metacluster 1/2










    







Motif 1/10










    







Motif hCWMSeqlets










    







Motif 2/10










    







Motif hCWMSeqlets










    







Motif 3/10










    







Motif hCWMSeqlets










    







Motif 4/10










    







Motif hCWMSeqlets










    







Motif 5/10










    







Motif hCWMSeqlets










    







Motif 6/10










    







Motif hCWMSeqlets










    







Motif 7/10










    







Motif hCWMSeqlets










    







Motif 8/10










    







Motif hCWMSeqlets










    







Motif 9/10










    







Motif hCWMSeqlets










    







Motif 10/10










    







Motif hCWMSeqlets










    







Metacluster 2/2










    







Motif 1/2










    







Motif hCWMSeqlets










    







Motif 2/2










    







Motif hCWMSeqlets