-
Notifications
You must be signed in to change notification settings - Fork 889
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.
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
ImageFeaturePlot can not show when data is huge #7505
Comments
Hi, it was tested on a number of Vizgen data. (Note: that is NOT Seurat V5) |
My segmentation data are json files, and I can be sure that there is no problem with my data reading. For the tutorial data, ImageFeaturePlot works well, I can do other plot such as "FeaturePlot(vizgen.obj,features = c('CD1C'))", and "ImageDimPlot(vizgen.obj, fov = "BC", cols = "Set3", axes = TRUE,size = 0.3,alpha = 0.5)". However, for ImageFeaturePlot, i do it by "ImageFeaturePlot(vizgen.obj, fov = "BC", features = "PECAM1")", only got axes and a black backgroud. |
Try non capital letters for gene names, like you did with `Set3`, ie, would be `Pecam1`.
As for the coord scale, if you load Vizgen data, then those will be in microns units for the axes
|
@Chaosli98 While |
Hi,
First of all, thank you for developing such a great tool! I am new to seurat V5, and i just start to use this for MERSCOPE data. So far I've been able to reproduce the tutorial data pretty well, which is only 80,000 cells.
However, I recently got more than 800, 000 cells in a slice, and I couldn't get any gene expression in any one cell when I used ImageFeaturePlot, just got axes and a black backgroud. I sure that the genes were fine, and the other drawing features including ImageDimPlot and FeaturePlot worked fine. Is it because there are too many cells? Any suggestions for how to deal with it?
Thanks!
Jin
The text was updated successfully, but these errors were encountered: