Explore - Understanding Compass Predictions by CRMap
The purpose of Explore is to provide users with insights into how Compass predicts patient responses to ICI treatment. We provide the Compass Response Map (CRMap) visualization tool, which allows you to explore the decision-making process, from gene expression data to the final probability predictions.
We offer the CRMap visualization site for the IMvigor210 cohort predictions. The model is trained on data excluding IMvigor210, and this visualization helps us understand the transformation from gene expression to final probabilities. You can access the visualization at the link below:
Click the RUN button on the sidebar after entering the parameters to generate the CRMap as shown below:
Example: Compass Response Map (CRMap)
The visualization offers several configurable parameters. Below is a table listing these parameters, their default values, and descriptions.
1. Patients Selection Paramters
| Parameter Name | Default Value | Description |
|---|---|---|
| Cancer Type | BLCA | Select one of 33 cancer types to filter patients. |
| Cohort | IMVigor210 | Select one of 16 cohorts to filter patients. |
| Immune Phenotype | Inflamed | Filter patients by immune phenotype (Inflamed, Desert, Excluded). |
| Response Label | Responder (R) | Filter patients by their clinical response label. |
| Compass Prediction | Responder (≥ 0.5) | Filter patients based on Compass prediction probability. |
| Select Sample ID | SAM203dcf14f927 | Select the Patient smaple id for Compass Response Map (CRMap) visulization |
2. Data Option Parameters
| Parameter Name | Default Value | Description |
|---|---|---|
| Concept to Plot | Cytotoxic_Tcell, Exhausted_Tcell, NKcell, etc. | Select one or more immune concepts for visualization. |
| TopK Gene | 1 | Set the number of top genes of each geneset to include in the visualization. |
3. Draw Option Parameters
| Parameter Name | Default Value | Description |
|---|---|---|
| Figure Width | 16 inches | Set the width of the visualization figure. |
| Figure Height | 13 inches | Set the height of the visualization figure. |
| Font Size | 15 | Set the font size for labels. |
| Layer Node Sizes | [0.5, 0.5, 1, 3, 5] | Set the node sizes for different layers, in JSON format. |
| Max Radial (max_rad) | 0.25 | Set the maximum radial curvature of arcs. |
| Show Geneset Name | False | Toggle to display geneset names in the visualization. |
| Layer Node Gaps | {"celltype": 0.15, "geneset": 0.1, "output": 0.2} | Set the spacing between nodes in layers, in JSON format. |
| Node Label Alignments | {"genetpm": -0.01, "gene": -0.01, "geneset": 0.01, "celltype": 0.02, "output": 0.02} | Configure alignment for node labels in JSON format. |
| Layer Edge Styles | {"celltype->output": {"linestyle": "--", "arrowstyle": "-"}} | Set edge styles between layers, in JSON format. |
| Genetpm Node Color Map | {"cmap": None, "vmin": -2, "vmax": 2} | Set the color map for genetpm nodes, in JSON format. |
| Compass Node Color Map | {"cmap": None, "vmin": 0, "vmax": 1} | Set the color map for compass nodes, in JSON format. |
| Label Threshold | {"genetpm": 0.5, "gene": 0.5, "geneset": 0.5, "celltype": -10, "output": -10} | Configure label visibility thresholds, in JSON format. |
| Label Color Same As Node | True | Configure label colors, if not same as node, use the black color |
| Layer Spacing | [1.2, 1.2, 1, 1] | Set the spacing between layers, in JSON format. |
| Genetpm->Gene Edge Colormap | {"cmap": None, "vmin": 0.6, "vmax": 1.0} | Set the colormap for genetpm-to-gene edges, in JSON format. |
| Genetpm->Gene Edge Threshold | 0.6 | To show edges with weights above the threshold. |
| Projector Edge Colormap | {"cmap": None, "vmin": 0.0, "vmax": 0.5} | Set the colormap for projector edges, in JSON format. |
| Edge Line Width | [0.2, 0.3, 0.3, 0.5] | Set line width for edges in layers, in JSON format. |
| Edge Activate | {"threshold": 10, "color": "red"} | Configure edge activation settings, in JSON format. |