cafferychen777
commented
1 year ago Hi, based on your description, it seems that you are using an outdated version of the ggpicrust2 package. The latest version of ggpicrust2 (v1.5.0) has fixed some issues with pathway_heatmap() and allows it to properly handle categorical metadata and normalization. I would suggest upgrading to the latest version of ggpicrust2 and retry it.
RayKramp1 @.***>于2023年4月5日 周三00:57写道：
here is my metadata metadata2.csv https://github.com/cafferychen777/ggpicrust2/files/11150999/metadata2.csv
and my ko adundances HPabun.csv https://github.com/cafferychen777/ggpicrust2/files/11151001/HPabun.csv
code for map: heatmap_plot <- pathway_heatmap(t(SAUN_matrix), metadata, "CST") print(heatmap_plot)
what I get [image: image] https://user-images.githubusercontent.com/129691560/229863315-e087a8be-d6a0-400f-ad95-0ae0a9f5cd01.png
it doesn't have CST and isn't normalized
what it looks like when I normalize with ggplot: [image: image] https://user-images.githubusercontent.com/129691560/229863494-a8864491-e1a7-4334-bde8-fa008dedaa8b.png
trying to figure out what is happening
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here is my metadata metadata2.csv
and my ko adundances HPabun.csv
code for map: heatmap_plot <- pathway_heatmap(t(SAUN_matrix), metadata, "CST") print(heatmap_plot)
what I get
it doesn't have CST and isn't normalized
what it looks like when I normalize with ggplot:
trying to figure out what is happening