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About the Subset out anatomical regions in Seurat v3.1.2 #2454

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BioAIEvolu opened this issue Dec 24, 2019 · 4 comments
Closed

About the Subset out anatomical regions in Seurat v3.1.2 #2454

BioAIEvolu opened this issue Dec 24, 2019 · 4 comments

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@BioAIEvolu
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Hi~I meet some problem in Subset out anatomical regions

I use the dataset: Mouse Brain Section (Coronal), and run sapceranger successfully,and get clustering_visualization img.

clustering_visualization.png

Then, everything run smoothly before Subset out anatomical regions.Howerver,I choose the the cluster of cortex for subsetting like this:

#Subset out anatomical regions
cortex <- subset(brain, idents = c(0, 1, 2, 5, 10, 11, 12 ))
# now remove additional cells, use SpatialDimPlots to visualize what to remove
# SpatialDimPlot(cortex,cells.highlight = WhichCells(cortex, expression = image_imagerow > 400 |
# image_imagecol < 150))
cortex <- subset(cortex, imgine_imagerow > 400 | image_imagecol < 150, invert = TRUE)
cortex <- subset(cortex, image_imagerow > 275 & image_imagecol > 370, invert = TRUE)
cortex <- subset(cortex, image_imagerow > 250 & image_imagecol > 440, invert = TRUE)

then, the error occur:

> #Subset out anatomical regions
> cortex <- subset(brain, idents = c(0, 1, 2, 5, 10, 11, 12 ))
> # now remove additional cells, use SpatialDimPlots to visualize what to remove
> # SpatialDimPlot(cortex,cells.highlight = WhichCells(cortex, expression = image_imagerow > 400 |
> # image_imagecol < 150))
> cortex <- subset(cortex, imgine_imagerow > 400 | image_imagecol < 150, invert = TRUE)
Error in FetchData(object = object, vars = expr.char[vars.use], cells = cells,  : 
  None of the requested variables were found: 
> cortex <- subset(cortex, image_imagerow > 275 & image_imagecol > 370, invert = TRUE)
Error in FetchData(object = object, vars = expr.char[vars.use], cells = cells,  : 
  None of the requested variables were found: 
> cortex <- subset(cortex, image_imagerow > 250 & image_imagecol > 440, invert = TRUE)
Error in FetchData(object = object, vars = expr.char[vars.use], cells = cells,  : 
  None of the requested variables were found:

And I have try to use the solution: #1212 (comment) for subsetting on features that have a dash in their name. But it doesn't work.

So,I wonder the structure of seurat may be the key to solve the problem.
I tape:

cortex@images

and saw：

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

Slot "coordinates":
                   tissue row col imagerow imagecol
AAACAATCTACTAGCA-1      1   3  43     1611     4170
AAACACCAATAACTGC-1      1  59  19     8315     2519
AAACAGAGCGACTCCT-1      1  14  94     2927     7679

I try change the imgine_imagerow into imagerow, and change the image_imagecol into the imagecol,but it doesn't work again.

And another question is : How can I further segment based on exact positions?

Because I don't know exactly about the coordinates of cortex.How the example in official website actually do in this step?

thanks!
@LucaMarconato
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same problem here

@andrewwbutler
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Collaborator

Hi,

Please try replacing image_imagerow and image_imagecol with anterior1_imagerow and anterior1_imagecol.

This is still under active development but the do.identify parameter of SpatialDimPlot should allow you to select cells manually or at least give you a sense of where you could start to draw some cutoffs.

@BioAIEvolu
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Thank you for your answer! Let me try again :-)

@FADHLyemen
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This solve it for me

SpatialDimPlot(cortex,cells.highlight = WhichCells(cortex, expression = slice1_imagerow > 10000
| slice1_imagecol > 100))

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@LucaMarconato @andrewwbutler @FADHLyemen @BioAIEvolu