initial app

app.py

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+import datasets
+import streamlit as st
+from st_aggrid import AgGrid, GridOptionsBuilder, JsCode
+
+st.set_page_config(layout='wide')
+
+# parse out gene_ids from URL query args to it's possible to link to this page
+query_params = st.query_params
+if "gene_id" in query_params.keys():
+    gene_id = query_params["gene_id"]
+else:
+    gene_id = "TGME49_231630"
+
+
+st.markdown("""
+# ToxoCEN Top50 co-expressed partners
+
+**ToxoCEN** is a co-expression network for *Cryptococcus neoformans* built on 719 RNA-seq runs across 39 studies.
+A pair of genes are said to be co-expressed when their expression is correlated across different conditions and
+is often a marker for genes to be involved in similar processes. 
+
+To Cite:<br>
+CS Arnold, Y Wang, VB Carruthers, MJ O'Meara ToxoCEN: A Co-Expression Network for Toxoplasma gondii
+* Code available at https://github.com/maomlab/CalCEN/tree/master/vignettes/ToxoCEN
+* Full network and dataset: https://huggingface.co/datasets/maomlab/ToxoCEN
+
+## Look up top-coexpressed partners:
+Put in the ``TGME49_######`` gene_id for a gene and expand the table to get the top 50 co-expressed genes.
+``coexp_score`` ranges between ``[0-1]``, where ``1`` is the best and greater than ``0.85`` can be considered significant.
+""")
+
+top_coexp_hits = datasets.load_dataset(
+    path = "maomlab/ToxoCEN",
+    data_files = {"top_coexp_hits": "top_coexp_hits.tsv"})
+top_coexp_hits = top_coexp_hits["top_coexp_hits"].to_pandas()
+
+col1, col2, col3 = st.columns(spec = [0.3, 0.2, 0.5])
+with col1:
+    gene_id = st.text_input(
+        label = "Gene ID",
+        value = f"{gene_id}",
+        max_chars = 10,
+        help = "TGME49 Gene ID e.g. CTGME49_231630")
+
+top_coexp_hits = top_coexp_hits[
+    top_coexp_hits.gene_id_1 == gene_id]
+top_coexp_hits = top_coexp_hits[[
+    'gene_id_1', 'gene_name_1', 'description_1',
+    'gene_id_2', 'gene_name_2', 'description_2',
+    'coexp_score', 'blastp_EValue']]
+top_coexp_hits["scatter_link"] = top_coexp_hits.apply(
+    lambda row: f"https://huggingface.co/spaces/maomlab/ToxoCEN-ExpressionScatter?gene_id_1={row.gene_id_1}&gene_id_2={row.gene_id_2}",
+    axis = 1)
+
+top_coexp_hits.reset_index()
+
+with col2:
+    st.text('') # help alignment with input box
+    st.download_button(
+        label = "Download data as TSV",
+        data = top_coexp_hits.to_csv(sep ='\t').encode('utf-8'),
+        file_name = f"top_coexp_hits_{gene_id}.tsv",
+        mime = "text/csv")
+
+# third column is padding only
+
+
+######### Table #########
+
+fungidb_link_renderer = JsCode("""
+        class UrlCellRenderer {
+          init(params) {
+            this.eGui = document.createElement('a');
+            this.eGui.innerText = params.value;
+            this.eGui.setAttribute('href', "https://toxodb.org/toxo/app/record/gene/" + params.value);
+            this.eGui.setAttribute('style', "text-decoration:none");
+            this.eGui.setAttribute('target', "_blank");
+          }
+          getGui() {
+            return this.eGui;
+          }
+        }
+""")
+
+coexp_scatter_link_renderer = JsCode("""
+        class UrlCellRenderer {
+          init(params) {
+            this.eGui = document.createElement('a');
+            this.eGui.innerText = 'plot';
+            this.eGui.setAttribute('href', params.value);
+            this.eGui.setAttribute('style', "text-decoration:none");
+            this.eGui.setAttribute('target', "_blank");
+          }
+          getGui() {
+            return this.eGui;
+          }
+        }
+""")
+
+
+
+grid_option_builder = GridOptionsBuilder()
+grid_option_builder.configure_auto_height()
+grid_option_builder.configure_default_column(
+    filterable=False,
+    groupable=False,
+    editable=False,
+    wrapText=True,
+    autoHeight=True)
+grid_option_builder.configure_column("gene_id_1", header_name="GeneID 1", pinned="left", cellRenderer=fungidb_link_renderer, width=550)
+grid_option_builder.configure_column("gene_name_1", header_name="Gene 1", pinned="left", width=500)
+grid_option_builder.configure_column("description_1", header_name="Description 1", width=1600)
+grid_option_builder.configure_column("gene_id_2", header_name="GeneID 2", pinned="left", cellRenderer=fungidb_link_renderer, width=550)
+grid_option_builder.configure_column("gene_name_2", header_name="Gene 2", pinned="left", width=500)
+grid_option_builder.configure_column("description_2", header_name="Description 2", width=1600)
+grid_option_builder.configure_column(
+    "coexp_score",
+    header_name="Coexp Score",
+    type=["numericColumn", "customNumericFormat"],
+    precision=3,
+    width=600)
+grid_option_builder.configure_column(
+    "blast_EValue",
+    header_name="Blast E-value",
+    type=["numericColumn", "customNumericFormat"],
+    precision=3,
+    width=600)
+grid_option_builder.configure_column(
+    "scatter_link",
+    header_name="Expression Scatterplot",
+    cellRenderer=coexp_scatter_link_renderer,
+    width=550)
+
+grid_option_builder.configure_selection(selection_mode=False, use_checkbox=False)
+
+AgGrid(
+    data = top_coexp_hits,
+    gridOptions = grid_option_builder.build(),
+    fit_columns_on_grid_load=True,
+    theme="streamlit",
+    allow_unsafe_jscode=True)