SpatialFeaturePlot and SpatialDimplot cannot show the expressed dot

[gucascau]

I lately updated the Seurat and several other R package but realized that the spatial figure no only show the expression details.

Here is an example. any idea? Thanks.

[dcollins15]

Please try setting the pt.size.factor parameter (something large). The way scaling is calculated was updated in v5.1.0 - if you'd like help debugging the issue further, please show us the output of ScaleFactors(object[["slice1"]].

[doctorchenzx]

Same here.
This is my output of ScaleFactors. Please help me.

ScaleFactors(new.C15[["inmage"]])
$spot
[1] 0.06818027

$fiducial
[1] 384.2371

$hires
[1] 0.06818027

$lowres
[1] 0.02045408

attr(,"class")
[1] "scalefactors"

[dcollins15]

@doctorchenzx have you tried setting pt.size.factor?

It looks like the scale factors have been manually changed - it's very surprising that hires and spot have the same value and that fiducial is orders of magnitude larger than any of the other values.

You can probably resolve the issue by updating the lowres value to match fiducial or else setting pt.size.factor to account for the difference between the two (i.e 384/0.02)

[doctorchenzx]

@doctorchenzx have you tried setting pt.size.factor?

It looks like the scale factors have been manually changed - it's very surprising that hires and spot have the same value and that fiducial is orders of magnitude larger than any of the other values.

You can probably resolve the issue by updating the lowres value to match fiducial or else setting pt.size.factor to account for the difference between the two (i.e 384/0.02)

Appreciate! I set pt.size.factor = 10000, and it looks cool.

[annaminyifeng]

Is there a recommended pt.size.factor Slide-seq objects? The ScaleFactors function seems like its only applicable to Visium objects.