Skip to content

Add cell layer only option #107

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 2 commits into
base: main
Choose a base branch
from
Open

Add cell layer only option #107

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
75ae78c
feat(viz): support cell-layer-only view
cornhundred Jul 1, 2025
849291f
Disable close-up mode in cell-layer-only mode
cornhundred Jul 1, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 5 additions & 1 deletion docs/overview/file_formats.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -159,10 +159,14 @@ This file contains the configuration information about the dataset. See example
]
}
],
"image_format": ".webp"
"image_format": ".webp",
"cell_layer_only": false
}
```

Setting `cell_layer_only` to `true` will render only the cell layer without
transcripts, cell boundaries, or images.

#### Gene Metadata
The `gene_metadata.parquet` file contains gene level metadata including: average expression across all cells, standard deviation, max expression, proportion of cells with non-zero expression, and the color assigned to each gene. See example below:

Expand Down
7 changes: 5 additions & 2 deletions js/deck-gl/core/calc_viewport.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,11 @@ export const calc_viewport = async (
layers_obj,
viz_state
) => {
const { tile_size } = viz_state.img.landscape_parameters;
const max_tiles_to_view = 50;
const { tile_size, cell_layer_only } =
Copy link

Copilot AI Jul 1, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

The tile_size variable is destructured but not used in this function; consider removing it if it's unnecessary to avoid confusion.

Copilot uses AI. Check for mistakes.
viz_state.img.landscape_parameters;
// Setting max_tiles_to_view to 0 prevents close_up mode from
// being triggered, which avoids fetching sub-cellular parquet files
const max_tiles_to_view = cell_layer_only === true ? 0 : 50;
const zoomFactor = Math.pow(2, zoom);
const [targetX, targetY] = target;
const halfWidthZoomed = width / (2 * zoomFactor);
Expand Down
9 changes: 8 additions & 1 deletion js/viz/landscape_ist.js
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -273,6 +273,8 @@ export const landscape_ist = async (

await set_landscape_parameters(viz_state.img, base_url, viz_state.aws);

const cell_layer_only =
viz_state.img.landscape_parameters.cell_layer_only === true;
Copy link

Copilot AI Jul 1, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

[nitpick] Consider destructuring cell_layer_only alongside other landscape parameters at the top of the function to keep extraction logic consistent and avoid inline property access throughout the function.

Copilot uses AI. Check for mistakes.
const tmp_image_info = viz_state.img.landscape_parameters.image_info;

viz_state.vector_name_integer =
Expand Down Expand Up @@ -397,7 +399,12 @@ export const landscape_ist = async (

update_trx_layer_radius(layers_obj, trx_radius);

if (viz_state.umap.state === true) {
if (cell_layer_only) {
toggle_background_layer_visibility(layers_obj, false);
toggle_visibility_image_layers(layers_obj, false);
toggle_trx_layer_visibility(layers_obj, false);
toggle_path_layer_visibility(layers_obj, false);
} else if (viz_state.umap.state === true) {
toggle_background_layer_visibility(layers_obj, false);
toggle_visibility_image_layers(layers_obj, false);
toggle_trx_layer_visibility(layers_obj, false);
Expand Down
Loading