shaln

Sorry, I'm afraid not! I'm biologist turned bioinformatician (only familiar with R) in dire need for a tool like the cellBrowser :)

Hello, I have a follow-up question related to this issue: is there a way to extract the cell IDs for a selected subset of cells? Thank you!

Thought I'd add this in case it's helpful: I'm on the latest macOS 13.4.1 (updated just today before running updateR), and I also have this exact same issue.

I have tried the above suggestions but still getting the error. My group names are 'Control_D5', 'Control_D7', 'Control_D9'. I have also tried swapping the group names to the cluster numbers...

Hi @asif7adil, thanks for the suggestion! I'm afraid the same error still persists after trying that :( ``` > control_group control_group draw_trajectory_plot(space, progression_group = control_group, contour = TRUE) Error in...

Hi, thought I'd mention that I've been getting the same error too, though only when computing the initial state. Both with and without specifying the n_states. I was able to...

Hi @igrabski, I'm re-opening this issue as I've been having the same error as above with the current versions of `Seurat` v5.1.0, `SeuratObject` v5.0.2 and `Matrix` v1.6-5. The error persisted...

@parkjooyoung99 This is the code I used to first re-orient the PAGA plot to mimic the UMAP. ``` # Compare UMAP and PAGA layouts fig,axs=plt.subplots(1,2,figsize=(20,10), dpi=250) sc.pl.umap(control_sce, color='subclusters', ax=axs[0], show=False,...

Thanks @PauBadiaM for the clear explanation! It is very helpful indeed :) I have a separate but relevant question. I mentioned in my original post that I processed the scRNA-seq...