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HaojiaWu / plot1cell

A R package for advanced single cell data viz
MIT License
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UMAP overlap with circ #4

Open joe-jhou2 opened 12 months ago

joe-jhou2 commented 12 months ago

Screenshot 2023-06-02 at 11 29 36 AM Any parameter can adjust circle size?

HaojiaWu commented 12 months ago

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 commented 12 months ago

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 commented 12 months ago

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 commented 12 months ago

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.