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theMILOlab / SPATA2

A Toolbox for Spatial Gene Expression Analysis
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tissueOutlineIdentified(object) is not TRUE #114

Open MatteoRiva95 opened 2 months ago

MatteoRiva95 commented 2 months ago

Good morning everyone,

I am trying to use this command, in order to actually see the outlines of the tissue in my spatial:

tissue_outline <- ggpLayerTissueOutline(object = object)

But it returns this error:

Error in getTissueOutlineDf(object) : tissueOutlineIdentified(object) is not TRUE Called from: base::stopifnot(tissueOutlineIdentified(object))

I don't understand why. object is a spata2 object. Is it possible to solve this issue please?

Thank you so much!

kueckelj commented 2 months ago

Hi. Have you used object <- identifyTissueOutline(object) beforehand?

MatteoRiva95 commented 1 month ago

@kueckelj thank you so much for your reply! I did not use it because it is not present in the following tutorial:

https://themilolab.github.io/SPATA2/articles/spata-v2-spatial-trajectories.html

Still, I used your command suggestion (identifyTissueOutline), but it gives me back this error:

Error in SPATA2::identifyTissueOutline(.) : tissueSectionsIdentfied(object) is not TRUE

Thank you again for your help

kueckelj commented 1 month ago

Hey, sorry for the late reply. You need to run object <- identifyTissueSections(object) , first. Does it work then?

MatteoRiva95 commented 1 month ago

@kueckelj thank you for your reply. object <- identifyTissueSections(object) works, but unfortunately when I run tissue_outline <- SPATA2::ggpLayerTissueOutline(object = object), it returns this error again:

17:38:14 Using center to center distance to compute pixel scale factor. 17:38:14 Computing barcode spot distances. 17:38:36 Done. Error in getTissueOutlineDf(object) : tissueOutlineIdentified(object) is not TRUE

The lines I am running right now are just these two:

object <- SPATA2::identifyTissueSections(object) tissue_outline <- SPATA2::ggpLayerTissueOutline(object = object)

MatteoRiva95 commented 1 month ago

@kueckelj Sorry, I finally did it. I misunderstood what you meant and running these three lines:

object <- SPATA2::identifyTissueSections(object) object <- SPATA2::identifyTissueOutline(object) tissue_outline <- SPATA2::ggpLayerTissueOutline(object = object)

it finally works :) I only suggest to update the tutorial adding these two lines (identifyTissueOutline and identifyTissueSections) for other users too!

Thank you @kueckelj for your kind help