UMAP overlap with circ

[joe-jhou2]

Any parameter can adjust circle size?

[HaojiaWu]

Hi @mimisikai
You can play with the scale parameter in prepare_circlize_data. For example, you can reduce the scale value to 0.5 like this:

circ_data <- prepare_circlize_data(your_seu_obj, scale = 0.5)

[joe-jhou2]

Thanks. Fix it. But can I customize the color? I've tried to either give color as fine_map_cluster_color = c("#85660D", "#C4451C","#FFB79F", "#B00068","#F6222E","#FF9DA7") or fine_map_cluster_color_list = c("CD4-CD8-(1)" = "#85660D", "CD4-CD8-(2)" = "#C4451C", "CD4 Tcm/Naive" = "#FFB79F", "CD4 Tem" = "#B00068"). But neither works.

[HaojiaWu]

Can you check levels(your_seu_obj) and see what it returns?
You should be able to see your cluster ID. If not, pls set it to your cluster ID with Seurat function SetIdent.

[joe-jhou2]

Can you check levels(your_seu_obj) and see what it returns? You should be able to see your cluster ID. If not, pls set it to your cluster ID with Seurat function SetIdent.

After changing the "Colors" variable in prepare_circlize_data, the problem is fixed. But only the UMAP colors are synchronized. Far out tracker circle's colors aren't matching with UMAP color. How to fix it? And can I adjust the track's width and font size? Thanks.