add regulatory demo

.gitignore

@@ -1 +1,7 @@
 data
+getdemo
+libs
+etc
+app/assets
+
+getdemo-1.0.0.sif

.gitmodules

@@ -1,3 +1,3 @@
-[submodule "modules/proscope"]
-	path = modules/proscope
-	url = [email protected]:fuxialexander/proscope.git
+[submodule "modules/atac_rna_data_processing"]
+	path = modules/atac_rna_data_processing
+	url = [email protected]:fuxialexander/atac_rna_data_processing.git

Dockerfile

@@ -6,7 +6,8 @@ WORKDIR /app
 
 
 # Create a new environment using mamba with specified packages
-RUN micromamba install -n base -c conda-forge -c bioconda -y python=3.10 git pip biopython nglview tqdm matplotlib pandas xmlschema seaborn numpy py3Dmol 
+RUN micromamba install -n base -c conda-forge -c bioconda -y python=3.10 pip biopython nglview dash-bio tqdm matplotlib pygraphviz pandas openpyxl pyarrow python-box xmlschema seaborn numpy py3Dmol pyranges scipy pyyaml zarr numcodecs pybigwig networkx plotly pysam requests seqlogo MOODS urllib3 pyliftover gprofiler-official pyfaidx
+
 ARG MAMBA_DOCKERFILE_ACTIVATE=1
 # Activate the environment and install additional packages via pip
 RUN pip3 install gradio 
@@ -34,6 +35,9 @@ COPY --chown=$MAMBA_USER:$MAMBA_USER app /app/app
 RUN cd modules/proscope &&  \
     pip3 install .
 
+RUN cd modules/atac_rna_data_processing &&  \
+    pip3 install .
+
 WORKDIR /app
 
 # Make port 80 available to the world outside this container

README.md

@@ -25,6 +25,8 @@ git clone --recursive [email protected]:fuxialexander/getdemo.git
 cd getdemo
 docker pull fuxialexander/getdemo:latest
 docker run -it -v "/path/to/data:/data" --rm -p 7681:7681 fuxialexander/getdemo
+or
+singularity run  -w --bind /manitou/pmg/users/xf2217/getdemo:/app --bind /manitou/pmg/users/xf2217/demo_data:/data --bind /pmglocal/xf2217/tmp:/tmp --no-home --pwd /app getdemo
 ```
 The gradio interface will be available at http://127.0.0.1:7681, a sharable link will be printed in the terminal.
 
@@ -34,4 +36,4 @@ git clone --recursive [email protected]:fuxialexander/getdemo.git
 cd getdemo
 docker build -t getdemo .
 docker run -it -v "/path/to/data:/data" --rm -p 7681:7681 getdemo
-```
+```

app/main.py

@@ -1,29 +1,62 @@
-import glob
+#%%
+import argparse
 import os
 
-import argparse
 import gradio as gr
 import matplotlib.pyplot as plt
-from proscope.data import get_seq, get_genename_to_uniprot, get_lddt
+import pkg_resources
+from proscope.data import get_genename_to_uniprot, get_lddt, get_seq
+import pandas as pd 
+from dash_bio import Clustergram
+
 seq = get_seq()
 genename_to_uniprot = get_genename_to_uniprot()
 lddt = get_lddt()
+import sys
+from glob import glob
+
+import numpy as np
+from atac_rna_data_processing.config.load_config import load_config
+from atac_rna_data_processing.io.celltype import GETCellType
+from atac_rna_data_processing.io.nr_motif_v1 import NrMotifV1
 from proscope.af2 import AFPairseg
 from proscope.protein import Protein
 from proscope.viewer import view_pdb_html
 
-
+#%%
 args = argparse.ArgumentParser()
 args.add_argument("-p", "--port", type=int, default=7860, help="Port number")
 args.add_argument("-s", "--share", action="store_true", help="Share on network")
 args.add_argument("-d", "--data", type=str, default="/data", help="Data directory")
-args = args.parse_args()
-gene_pairs = glob.glob(f"{args.data}/structures/causal/*")
+# args = args.parse_args()
+# set pseudo args
+args = args.parse_args(['-p', '7869', '-s', '-d', '/manitou/pmg/users/xf2217/demo_data'])
+#%%
+gene_pairs = glob(f"{args.data}/structures/causal/*")
 gene_pairs = [os.path.basename(pair) for pair in gene_pairs]
-
+GET_CONFIG = load_config('/manitou/pmg/users/xf2217/atac_rna_data_processing/atac_rna_data_processing/config/GET')
+GET_CONFIG.celltype.jacob=True
+GET_CONFIG.celltype.num_cls=2
+GET_CONFIG.celltype.input=True
+GET_CONFIG.celltype.embed=True
+GET_CONFIG.celltype.data_dir = '/manitou/pmg/users/xf2217/pretrain_human_bingren_shendure_apr2023/fetal_adult/'
+GET_CONFIG.celltype.interpret_dir='/manitou/pmg/users/xf2217/Interpretation_all_hg38_allembed_v4_natac/'
+GET_CONFIG.motif_dir = '/manitou/pmg/users/xf2217/interpret_natac/motif-clustering'
+motif = NrMotifV1.load_from_pickle(
+    pkg_resources.resource_filename("atac_rna_data_processing", "data/NrMotifV1.pkl"),
+    GET_CONFIG.motif_dir
+)
+cell_type_annot = pd.read_csv(GET_CONFIG.celltype.data_dir.split('fetal_adult')[0] + 'data/cell_type_pretrain_human_bingren_shendure_apr2023.txt')
+cell_type_id_to_name = dict(zip(cell_type_annot['id'], cell_type_annot['celltype']))
+cell_type_name_to_id = dict(zip(cell_type_annot['celltype'], cell_type_annot['id']))
+avaliable_celltypes = sorted([cell_type_id_to_name[f.split('/')[-1]] for f in glob(GET_CONFIG.celltype.interpret_dir+'*')])
+#%%
+# fill this in...
 # set plot ppi to 100
 plt.rcParams['figure.dpi'] = 100
 
+
+
 def visualize_AF2(tf_pair, a):
     strcture_dir = f"{args.data}/structures/causal/{tf_pair}"
     fasta_dir = f"{args.data}/sequences/causal/{tf_pair}"
@@ -46,9 +79,45 @@ def view_pdb(seg_pair, a):
     return view_pdb_html(pdb_path), a, pdb_path
 
 
+
 def update_dropdown(x, label):
     return gr.Dropdown.update(choices=x, label=label)
 
+def load_and_plot_celltype(celltype_name, GET_CONFIG, cell):
+    celltype_id = cell_type_name_to_id[celltype_name]
+    cell = GETCellType(celltype_id, GET_CONFIG)
+    cell.celltype_name = celltype_name
+    gene_exp_fig = cell.plotly_gene_exp()
+    gene_exp_table = cell.gene_annot.groupby('gene_name')[['pred', 'obs', 'accessibility']].mean().reset_index()
+    return gene_exp_fig, gene_exp_table, cell
+    
+def plot_gene_regions(cell, gene_name, plotly=True):
+    return cell.plot_gene_regions(gene_name, plotly=plotly), cell
+
+def plot_gene_motifs(cell, gene_name, motif, overwrite=False):
+    return cell.plot_gene_motifs(gene_name, motif, overwrite=overwrite)[0], cell
+
+def plot_motif_subnet(cell, motif_collection, m, type='neighbors', threshold=0.1):
+    return cell.plotly_motif_subnet(motif_collection, m, type=type, threshold=threshold), cell
+
+def plot_gene_exp(cell, plotly=True):
+    return cell.plotly_gene_exp(plotly=plotly), cell
+
+def plot_motif_corr(cell):
+    fig = Clustergram(data=cell.gene_by_motif.corr,
+                    column_labels=list(cell.gene_by_motif.corr.columns.values),
+                    row_labels=list(cell.gene_by_motif.corr.index),
+                    hidden_labels=['row', 'col'],
+                    link_method='average',
+                    display_ratio=0.1,
+                    width=600,
+                    height=400,
+                    color_map='rdbu_r',
+                    )
+    return fig, cell
+
+#%%
+# fill this in...
 
 # main
 if __name__ == '__main__':
@@ -56,10 +125,50 @@ if __name__ == '__main__':
 
         seg_pairs = gr.State([''])
         af = gr.State(None)
+        cell = gr.State(None)
+        
         with gr.Row() as row:
+            # Left column: Plot gene expression and gene regions
             with gr.Column():
-                tf_pairs = gr.Dropdown(label='TF pair', choices=gene_pairs)
-                tf_pairs_btn = gr.Button(value='Load & Plot')
+                with gr.Row() as row:
+                    celltype_name = gr.Dropdown(label='Cell Type', choices=avaliable_celltypes)  
+                    celltype_btn = gr.Button(value='Load & Plot Gene Expression')
+                gene_exp_plot = gr.Plot(label='Gene Expression Pred vs Obs')
+                gene_exp_table = gr.DataFrame(label='Gene Expression Table', max_rows=10)
+                
+            # Right column: Plot gene motifs
+            with gr.Column():
+                gene_name_for_region = gr.Textbox(label='Get important regions or motifs for gene:')
+                with gr.Row() as row:
+                    region_plot_btn = gr.Button(value='Regions')
+                    motif_plot_btn = gr.Button(value='Motifs')
+
+                region_plot = gr.Plot(label='Gene Regions')
+                motif_plot = gr.Plot(label='Gene Motifs')
+
+        
+        with gr.Row() as row:
+            with gr.Column():
+                clustergram_btn = gr.Button(value='Plot Motif Correlation Heatmap')
+                clustergram_plot = gr.Plot(label='Motif Correlation')
+
+            
+            # Right column: Motif subnet plot
+            with gr.Column():
+                with gr.Row() as row:
+                    motif_for_subnet = gr.Dropdown(label='Motif Causal Subnetwork', choices=motif.cluster_names)
+                    subnet_type = gr.Dropdown(label='Type', choices=['neighbors', 'parents', 'children'], default='neighbors')
+                    # slider for threshold 0.01-0.2
+                    subnet_threshold = gr.Slider(label='Threshold', minimum=0.01, maximum=0.25, step=0.01, value=0.1)
+                subnet_btn = gr.Button(value='Plot Motif Causal Subnetwork')
+                subnet_plot = gr.Plot(label='Motif Causal Subnetwork')
+                
+
+        with gr.Row() as row:
+            with gr.Column():
+                with gr.Row() as row:
+                    tf_pairs = gr.Dropdown(label='TF pair', choices=gene_pairs)
+                    tf_pairs_btn = gr.Button(value='Load & Plot')
                 interact_plddt1 = gr.Plot(label='Interact pLDDT 1')
                 interact_plddt2 = gr.Plot(label='Interact pLDDT 2')
                 protein1_plddt = gr.Plot(label='Protein 1 pLDDT')
@@ -68,13 +177,21 @@ if __name__ == '__main__':
                 heatmap = gr.Plot(label='Heatmap')
             
             with gr.Column():
-                segpair = gr.Dropdown(label='Seg pair', choices=seg_pairs.value)
-                segpair_btn = gr.Button(value='Get PDB')
+                with gr.Row() as row:
+                    segpair = gr.Dropdown(label='Seg pair', choices=seg_pairs.value)
+                    segpair_btn = gr.Button(value='Get PDB')
                 pdb_html = gr.HTML(label="PDB HTML")
                 pdb_file = gr.File(label='Download PDB')
 
         tf_pairs_btn.click(visualize_AF2, inputs = [tf_pairs, af], outputs = [ interact_plddt1, interact_plddt2, protein1_plddt, protein2_plddt, heatmap, segpair, af])
         segpair_btn.click(view_pdb, inputs=[segpair, af], outputs=[pdb_html, af, pdb_file])
+        celltype_btn.click(load_and_plot_celltype, inputs=[celltype_name, gr.State(GET_CONFIG), cell], outputs=[gene_exp_plot, gene_exp_table, cell])
+        region_plot_btn.click(plot_gene_regions, inputs=[cell, gene_name_for_region], outputs=[region_plot, cell])
+        motif_plot_btn.click(plot_gene_motifs, inputs=[cell, gene_name_for_region, gr.State(motif)], outputs=[motif_plot, cell])
+        clustergram_btn.click(plot_motif_corr, inputs=[cell], outputs=[clustergram_plot, cell])
+        subnet_btn.click(plot_motif_subnet, inputs=[cell, gr.State(motif), motif_for_subnet, subnet_type, subnet_threshold], outputs=[subnet_plot, cell])
 
     demo.launch(share=args.share, server_port=args.port)
 
+
+# %%

modules/atac_rna_data_processing

@@ -0,0 +1 @@
+Subproject commit fc337002918de1e5f1f864e7ba94864a743fd16c

modules/proscope

@@ -1 +0,0 @@
-Subproject commit fdb98d02f0d2345a74f28e71211849992893fa5d