CellSR.o not showing the tsne plot and DoDiffusionMap.o$root is not calculated about landscent HOT 4 CLOSED

Hi,

Did you check if the SR are all properly calculated? Because if you set the input argument as root = c("cell", "state"), the root will be selected as the cell with maximum SR value. So if the SR of all cells are not correctly computed, the selection step will be interfered.

And from the plot you show above, it seems the SR values are not shown, although the legend gives the range of SR...It is a bit wired.

So maybe you need to check the SR values first and to see if they are all correct.

And I may then help you further.

Best,
Weiyan

from landscent.

Thank you for the quick reply.

I checked the SR (Is it right by anyNA(SR.total$SR)?) and it returned FALSE.
I can calculate and show Plot_LandSR with pre-calculated tsne coordinates by Seurat normally, so it is very strange for me not show Plot_CellSR.

Thank you.

from landscent.

Hi,

Sometimes, Plot_CellSR cannot show the lower flat panel is because the argument num_grid is not properly set. You probably need to try other values.

But it is strange to me that you cannot select the root, however you get all SR values calculated.

Best,
Weiyan

from landscent.

Thank you.

I changed the num_grid and I could show the Plot_CellSR, but very rough plot.

Also, I tried again to calculate DoDiffusionMap and it succeeded to plot (but I do not know why).

Thank you for your advice!.

from landscent.