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navinlabcode / CellTrek

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Disorder coordiantes for 10x visium data. #9

Closed zhou-ran closed 2 years ago

zhou-ran commented 2 years ago

Hi all,

I perform CellTrek on my unpublised 10x visium data with default parameters, but the predicted coordinate for each single cell couldn't match to the HE picture, here is the shiny plot.

image

Best, Ran

WandeRum commented 2 years ago

Hi Ran. It looks like a repelling problem. What are your repel_r and repel_iter parameters? You can probably set them to a smaller number like 5, 10, respectively. U can also check DimPlot(obj, reduction='celltrek_raw').

zhou-ran commented 2 years ago

Hi, Thanks for your advice, problem was solved perfectly by choosing smaller repel value. Ran

PaulaNietoG commented 2 years ago

Hello, I'm having the same issue when using celltrek_vis. However, I am not able to correctly implement the changes in the repel_x and repel_iter, as I see no changes on the plot. Could you provide an example of how to update these two parameters? Thanks