add html report

Author: yztxwd

test/test_cav_trainer.py

@@ -6,7 +6,7 @@
 from Bio import motifs as Bio_motifs
 from captum.attr import DeepLift
 
-from tpcav import helper, run_tpcav, utils
+from tpcav import helper, run_tpcav, utils, report
 from tpcav.cavs import CavTrainer
 from tpcav.concepts import ConceptBuilder
 from tpcav.tpcav_model import TPCAV, _abs_attribution_func
@@ -118,6 +118,10 @@ def test_run_tpcav_random_control(self):
             output_dir="data/test_run_tpcav_output/",
         )
 
+        report.generate_tcav_html_report("data/test_html.html", motif_cav_trainers,
+                                         extra_cav_trainers = {'repeats': bed_cav_trainer},
+                                         motif_file=motif_path, fscore_thresh=0.1)
+
     def test_run_tpcav_consensus_random_control(self):
         motif_path = Path("data") / "custom_motifs_alan.tsv"
         genome_fasta = "data/hg38.analysisSet.fa"

tpcav/cavs.py

@@ -419,7 +419,7 @@ def plot_cavs_similaritiy_heatmap(
         cm = sns.clustermap(
             matrix_similarity,
             xticklabels=False,
-            yticklabels=False,
+            yticklabels=False if attributions is not None else cavs_names_pass,
             cmap="bwr",
             vmin=-1,
             vmax=1,
@@ -462,15 +462,20 @@ def plot_cavs_similaritiy_heatmap(
 
         # plot motif logo if provided meme file, try to look for pwm for every concept in the file
         if motif_meme_file is not None:
-            ax_logs[-1].tick_params(
-               axis="y", which="major", pad=cm.figure.get_size_inches()[0] * 0.2 * 72 # leave space for motif logos
-            )
+            if attributions is not None:
+                ax_logs[-1].tick_params(
+                   axis="y", which="major", pad=cm.figure.get_size_inches()[0] * 0.3 * 72 # leave space for motif logos
+                )
+            else:
+                cm.ax_heatmap.tick_params(
+                   axis="y", which="major", pad=cm.figure.get_size_inches()[0] * 0.3 * 72 # leave space for motif logos
+                )
             gs_logo = gridspec.GridSpec(len(cavs_names_pass), 1)
 
             logo_height = heatmap_bbox.height/len(cavs_names_pass)
             for i, (cav_key, g) in enumerate(zip(cavs_names_sorted[::-1], gs_logo)):
                 ax_logo = plt.subplot(g)
-                ax_logo.set_position([1+len(ax_logs)*0.2+0.01, heatmap_bbox.y0+i*logo_height, 0.2+0.01, logo_height])
+                ax_logo.set_position([1+len(ax_logs)*0.2+0.01, heatmap_bbox.y0+i*logo_height, 0.3+0.01, logo_height])
                 if cav_key is not None:
                     seq_logo(cav_key, motif_meme_file=motif_meme_file, ax=ax_logo)
                 else: