Skip to content

Commit

Permalink
rasterize heatmap in vignette
Browse files Browse the repository at this point in the history
A rasterized version of the incoming signal heatmap is rendered to avoid a figure too large to render in the vignette.
  • Loading branch information
jmitchell81 committed Dec 6, 2023
1 parent f4e060d commit b7f624e
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion vignettes/domino2.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -472,7 +472,7 @@ gene_network(pbmc_dom, clust = 'dendritic_cell', OutgoingSignalingClust = "CD14_
A comprehensive assessment of ligand expression targeting active receptors on a given cluster can be assessed with `incoming_signaling_heatmap()`.

```{r}
incoming_signaling_heatmap(pbmc_dom, rec_clust = 'dendritic_cell', max_thresh = 2.5)
incoming_signaling_heatmap(pbmc_dom, rec_clust = 'dendritic_cell', max_thresh = 2.5, use_raster = TRUE)
```

Another form of comprehensive ligand expression assessment is available for individual active receptors in the form of circos plots new to domino2. The outer arcs correspond to clusters in the domino object with inner arcs representing each possible ligand of the plotted receptor. Arcs are drawn between ligands on a cell type and the receptor if the ligand is expressed above the specified threshold. Arc widths correspond to the mean express of the ligand by the cluster with the widest arc width scaling to the maximum expression of the ligand within the data.
Expand Down

0 comments on commit b7f624e

Please sign in to comment.