SpatialDecon with Visium error

[chrkuo]

Thank you so much for creating this wonderful tool. I am utilizing spatialdecon to estimate the cell fractions of each spatial spot in my visium 10x tumor sample.

from reading your vignette there seems to be a few limitations with using visium data in spatialdecon.

I have encountered an error as I was trying to perform cell abundance estimates:

sharedgenes = intersect(rownames(raw), rownames(safeTME))
plot(colSums(raw), colSums(raw[sharedgenes, ]), log = "xy")

Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'plot': 'x' must be an array of at least two dimensions

I'm not sure how to get through this error and if it's just the nature of using visium data?

appreciate your assistance and thank you for your time

[maddygriz]

Hi @chrkuo,

Thank you for reaching out. Our customer support team will be able to help you with this. Please email support@nanostring.com with your issue.

Thanks,
Maddy

[chrkuo]

@maddygriz

I emailed the question and was told that code support will only be provided for the use of spatialdecon with geomx.

Is that true? In the spatialdecon paper it was utilized in visium samples.

Please advise

Thank you