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satijalab / seurat

R toolkit for single cell genomics
http://www.satijalab.org/seurat
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Question about ImageDimPlot function #9497

Open lidd77 opened 2 days ago

lidd77 commented 2 days ago

Hello, I run the following code ,

FetchData( obj[["fov"]][["molecules"]], vars = "Tagln")) and got the following result :

       x        y molecule
1 373.0469 1619.828    Tagln
2 383.9688 1631.656    Tagln
3 384.1406 1625.312    Tagln

I know "Tagln" means gene , could you tell me what the meaning of x/y coordinates is ? RNA position from this Tagln ?

and another question , 

 dim(FetchData(  obj[["fov"]][["molecules"]], vars = "Tagln"))  # return (30331,3) 
 ImageDimPlot(obj, fov = "fov", molecules = c("Tagln"), nmols = 20)

For the first line code , it returns (30331,3), so 30331 is the total number of RNA or Gene or other some stuff? I set nmols value 20 , so what does this number 20 mean ?

Expecting your reply !

Thank you very much !

Best

rharao commented 2 days ago

I know "Tagln" means gene , could you tell me what the meaning of x/y coordinates is ? RNA position from this Tagln ?

Yes, Tagln was detected at each of those x,y coordinates.

The dimensions (dim) of the matrix you requested (FetchData) are (30331, 3): 30,331 rows (molecules) by 3 columns (x-coordinate, y-coordinate, and molecule name for each molecule; in your case, because you only requested Tagln, the molecule name is the same for all.)

I set nmols value 20 , so what does this number 20 mean ?

See the reference page for ImageDimPlot:

nmols: Max number of each molecule specified in molecules to plot

So only twenty Tagln molecules or fewer are displayed on the plot.

lidd77 commented 1 day ago

The dimensions (dim) of the matrix you requested (FetchData) are (30331, 3): 30,331 rows (molecules) by 3 columns (x-coordinate, y-coordinate, and molecule name for each molecule; in your case, because you only requested Tagln, the molecule name is the same for all.)

Yeah, thank you .
So 30331 means 30331 Tagln genes for 21920 cells , the number of Tagln gene is bigger than the number of cells ? is it correct ?

rharao commented 1 day ago

Depending on the tissue and transcript, it is quite possible for there to be more reads for a transcript than there are cells in total; it just means that, on average, a cell has more than one copy of the transcript.