Merge All High Schoolers' PRs

.gitignore

@@ -1,3 +1,6 @@
+# Jupyter
+.ipynb_checkpoints/
+
 # Python
 __pycache__/
 *.py[cod]
@@ -65,4 +68,4 @@ SCSAWorkflow/
 # Security documentation (internal use only)
 SECURITY_DOCUMENTATION.md
 SECURITY_IMPLEMENTATION.md
-SECURITY_FIXES.md
+SECURITY_FIXES.md

CONTRIBUTING.md

@@ -0,0 +1,7 @@
+# Contributing
+
+Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given.
+
+Please refer to this copilot-based instructions for SPAC Shiny development: https://github.com/FNLCR-DMAP/SPAC_Shiny/blob/main/.github/copilot-instructions.md
+
+Also refer to this contributing guide in the SPAC Package project for more information: https://github.com/FNLCR-DMAP/SCSAWorkflow/blob/main/CONTRIBUTING.md

Dockerfile

@@ -1,9 +1,18 @@
 # Use official Python image as base
-FROM python:3.9.19-slim-bookworm
+# Fix: python version conflicts (Issue #15 in Purdue-2025 fork)
+# Error message when building docker:
+# Package 'datashader' requires a different Python: 3.9.19 not in '>=3.10'
+# FROM python:3.9.19-slim-bookworm
+FROM python:3.10-slim-bookworm
 
 # Set working directory
 WORKDIR /app
 
+# Fix: 'Hash Sum Mismatch' bug for mac device (Issue #12 in Purdue-2025 fork)
+RUN echo "Acquire::http::Pipeline-Depth 0;" > /etc/apt/apt.conf.d/99custom && \
+    echo "Acquire::http::No-Cache true;" >> /etc/apt/apt.conf.d/99custom && \
+    echo "Acquire::BrokenProxy    true;" >> /etc/apt/apt.conf.d/99custom
+
 # Install system dependencies needed for scientific packages
 RUN apt-get update && apt-get install -y \
     gcc \

README.md

@@ -63,8 +63,15 @@ This project was a success thanks to the invaluable collaboration and support fr
     *   Suriya Selvarajan
     *   Qianyue Wang
     *   Andree Kolliegbo
+    *   Sungmin Lee
+    *   Saran Nagubandi
+    *   Noah Lee
+    *   Boqiang Zhang
+    *   Heaven Golladay-Watkins
+    *   Arjun Chhabra
 *   **Teaching Assistants (TAs) from Purdue's Data Mine:**
     *   Alex Liu
     *   Omar Eldaghar
     *   Thomas Sheeley
+    *   Ramya Rajaram
 *   **Additional Support:** Kang Liu and Rui He, and the entire Data Mine staff.

environment.yml

@@ -1,11 +1,31 @@
+# Warning: 
+# This file may be outdated. Check with requirements.txt to get the latest environmental requirements.
+# This is a file for conda users to create an environment. 
+
+# Quick Guide:
+# 1. Make sure you are in the repository's directory and 'conda' is installed.
+# 2. Run 'conda env create -f environment.yml' to create the conda environment.
+# 3. Run 'conda activate shiny' to activate this environment.
+# 4. Run 'shiny run --reload app.py' to run the app.
+# The app will be available at http://127.0.0.1:8000.
+
+# Special Reminder:
+# For macOS (MacArm64) users, make these edits to the environment.yml file:
+# Under dependencies, add these lines:
+# - tables>=3.8.0
+# - c-blosc2
+# - libtiff
+# Under pip, remove this line:
+# - tables==3.8.0
+
 name: shiny
 channels:
   - ohsu-comp-bio
   - conda-forge
   - leej3
   - https://fnlcr-dmap.github.io/scimap/
 dependencies:
-  - python=3.9.13
+  - python=3.10.19  # To support datashader, need python>=3.10
   - numpy=1.26.4
   - pandas=1.5.3
   - anndata=0.10.9
@@ -18,20 +38,24 @@ dependencies:
   - squidpy=1.2.2
   - scikit-image=0.19.3
   - scipy=1.10.1
+  # For macOS (MacArm64) users, uncomment the following three lines
+  # - tables>=3.8.0
+  # - c-blosc2
+  # - libtiff
   - pip
   - pip:
       - ipykernel==6.29.5
       - ipython==8.18.0
       - ipython-genutils==0.2.0
-      - ipywidgets==8.1.3
+      - ipywidgets==8.1.7   # To be consistent with requirement.txt
       - jsonschema-specifications==2023.12.1
       - jupyter-events==0.10.0
       - jupyter_client==7.4.9
       - jupyter_core==5.7.2
       - jupyter_server==2.14.1
       - jupyter_server_terminals==0.5.3
       - jupyterlab_pygments==0.3.0
-      - jupyterlab_widgets==3.0.11
+      - jupyterlab_widgets==3.0.15    # To be consistent with requirement.txt
       - nbclient==0.10.0
       - nbconvert==7.16.4
       - nbformat==5.10.4
@@ -50,7 +74,7 @@ dependencies:
       - shinyswatch==0.6.1
       - shinywidgets==0.7.0
       - sinfo==0.3.4
-      - tables==3.8.0
+      - tables==3.8.0   # For macOS (MacArm64) users, comment out this line.
       - tinycss2==1.3.0
       - tqdm==4.66.4
       - typeguard==4.3.0
@@ -60,5 +84,11 @@ dependencies:
       - websockets==12.0
       - zipp==3.19.2
       - tifffile
+      - shapely==2.0.7  # To be consistent with requirement.txt
       - sag-py-execution-time-decorator @ git+https://github.com/SamhammerAG/sag_py_execution_time_decorator.git@976c9683d561aadc0166495117c42cc1762633d7
-      - spac @ git+https://github.com/FNLCR-DMAP/SCSAWorkflow.git@76f381316acd57ff9fbe3e5bea4e37b0a9ae3dd9#egg=spac
+      # Added: packages for heatmap mode in scatterplot
+      - colorcet
+      - git+https://github.com/holoviz/datashader.git
+      # SPAC package pinned to specific commit for template compatibility (dev branch as of 2025-10-15)
+      - spac @ git+https://github.com/FNLCR-DMAP/SCSAWorkflow.git@c2a248826b91880c62308e85e60cae9361c275d0#egg=spac
+

requirements.txt

@@ -52,5 +52,8 @@ zipp==3.19.2
 tifffile
 shapely==2.0.7
 sag-py-execution-time-decorator @ git+https://github.com/SamhammerAG/sag_py_execution_time_decorator.git@976c9683d561aadc0166495117c42cc1762633d7
+# Added: packages for heatmap mode in scatterplot
+colorcet
+git+https://github.com/holoviz/datashader.git
 # SPAC package pinned to specific commit for template compatibility (dev branch as of 2025-10-15)
 spac @ git+https://github.com/FNLCR-DMAP/SCSAWorkflow.git@c2a248826b91880c62308e85e60cae9361c275d0#egg=spac

server/anno_vs_anno_server.py

@@ -22,6 +22,15 @@ def spac_Sankey():
                 source_annotation=input.sk1_anno1(), 
                 target_annotation=input.sk1_anno2()
             )
+
+            font_size = input.sankey_font_size()
+
+            # Modified... 
+            # Applying font size directly to the Sankey trace for node and 
+            # label text, as the global layout font can sometimes be ignored.
+            fig.update_layout(font=dict(size=font_size))
+            fig.update_traces(textfont=dict(size=font_size), selector=dict(type='sankey'))
+
             return fig
         return None
 
@@ -40,6 +49,19 @@ def spac_Relational():
                 target_annotation=input.rhm_anno2()
             )
             shared['df_relational'].set(result['data'])
+
+            font_size = input.heatmap_font_size()
+
+            # Modified...
+            # Applying font size directly to the heatmap axes and color bar,
+            # as these elements often have their own font settings.
+            result['figure'].update_layout(
+                font=dict(size=font_size),
+                xaxis=dict(tickfont=dict(size=font_size)),
+                yaxis=dict(tickfont=dict(size=font_size))
+            )
+            result['figure'].update_coloraxes(colorbar_tickfont_size=font_size)
+
             return result['figure']
         return None
 

server/annotations_server.py

@@ -1,6 +1,8 @@
 from shiny import ui, render, reactive
 import numpy as np
 import spac.visualization
+# Added...
+import matplotlib.pyplot as plt
 
 def annotations_server(input, output, session, shared):
     @output
@@ -11,30 +13,38 @@ def spac_Histogram_2():
         if adata is None:
             return None
 
+        # Added...
+        # Note: This assumes your UI file has a slider with the id 'annotations_font_size'.
+        # Please ensure this ID matches the one in your annotations_ui.py file.
+        font_size = input.annotations_font_size()
+        plt.rcParams.update({'font.size': font_size})
+        rotation = input.anno_slider()
+
         # 1) If "Group By" is UNCHECKED, show a simple annotation histogram
         if not input.h2_group_by_check():
             fig, ax, df = spac.visualization.histogram(
                 adata,
                 annotation=input.h2_anno()
             ).values()
-            shared['df_histogram2'].set(df) 
-            ax.tick_params(axis='x', rotation=input.anno_slider(), labelsize=10)
+            shared['df_histogram2'].set(df)
+            # Modified...
+            ax.tick_params(axis='x', rotation=rotation, labelsize=font_size)
             return fig
 
-        # 2) If "Group By" is CHECKED, we must always supply a 
+        # 2) If "Group By" is CHECKED, we must always supply a
         #    valid multiple parameter
         else:
-            # If user also checked "Plot Together", use their selected 
+            # If user also checked "Plot Together", use their selected
             # stack type
             if input.h2_together_check():
                 # e.g. 'stack', 'dodge', etc.
-                multiple_param = input.h2_together_drop()  
+                multiple_param = input.h2_together_drop()
 
                 together_flag = True
             else:
                 # If grouping by but not "plot together", pick a default layout
                 # or 'dodge' or any valid string
-                multiple_param = "layer"  
+                multiple_param = "layer"
                 together_flag = False
 
             fig, ax, df = spac.visualization.histogram(
@@ -44,13 +54,15 @@ def spac_Histogram_2():
                 together=together_flag,
                 multiple=multiple_param
             ).values()
-            shared['df_histogram2'].set(df) 
+            shared['df_histogram2'].set(df)
             axes = ax if isinstance(ax, (list, np.ndarray)) else [ax]
-            for ax in axes:
-                ax.tick_params(
-                    axis='x', 
-                    rotation=input.anno_slider(), 
-                    labelsize=10
+            # Modified... (renamed loop variable to avoid shadowing)
+            for current_ax in axes:
+                # Modified...
+                current_ax.tick_params(
+                    axis='x',
+                    rotation=rotation,
+                    labelsize=font_size
                 )
             return fig
         return None
@@ -61,16 +73,16 @@ def spac_Histogram_2():
     def download_histogram_button_ui():
         if shared['df_histogram2'].get() is not None:
             return ui.download_button(
-                "download_histogram2_df", 
-                "Download Data", 
+                "download_histogram2_df",
+                "Download Data",
                 class_="btn-warning"
             )
         return None
 
 
     @render.download(filename="annotation_histogram_data.csv")
     def download_histogram2_df():
-        df = shared['df_histogram2'].get()
+        df = shared['df_human_histogram2'].get()
         if df is not None:
             csv_string = df.to_csv(index=False)
             csv_bytes = csv_string.encode("utf-8")
@@ -86,8 +98,8 @@ def histogram_reactivity_2():
 
         if btn and not ui_initialized:
             dropdown = ui.input_select(
-                "h2_anno_1", 
-                "Select an Annotation", 
+                "h2_anno_1",
+                "Select an Annotation",
                 choices=shared['obs_names'].get()
             )
             ui.insert_ui(
@@ -97,8 +109,8 @@ def histogram_reactivity_2():
             )
 
             together_check = ui.input_checkbox(
-                "h2_together_check", 
-                "Plot Together", 
+                "h2_together_check",
+                "Plot Together",
                 value=True
             )
             ui.insert_ui(
@@ -120,18 +132,18 @@ def histogram_reactivity_2():
     def update_stack_type_dropdown():
         if input.h2_together_check():
             dropdown_together = ui.input_select(
-                "h2_together_drop", 
-                "Select Stack Type", 
-                choices=['stack', 'layer', 'dodge', 'fill'], 
+                "h2_together_drop",
+                "Select Stack Type",
+                choices=['stack', 'layer', 'dodge', 'fill'],
                 selected='stack'
             )
             ui.insert_ui(
                 ui.div({
-                    "id": "inserted-dropdown_together-1"}, 
+                    "id": "inserted-dropdown_together-1"},
                     dropdown_together
                 ),
                 selector="#main-h2_together_drop",
                 where="beforeEnd"
-            )      
+            )
         else:
-            ui.remove_ui("#inserted-dropdown_together-1")
+            ui.remove_ui("#inserted-dropdown_together-1")