The imageSize parameter currently covers the entire image area.

[MAXTIAN-BU]

The imageSize parameter currently covers the entire image area. How Modify the code so that only the tissue region is covered:
SpaCET.visualize.spatialFeature(

• SpaCET_obj,
• spatialType = "QualityControl",
• spatialFeatures=c("UMI","Gene"), #
• imageBg = T,
• imageSize = "CaptureArea"，
• pointSize = 2)#

[beibeiru]

Hi, @MAXTIAN-BU

Thank you for your interest in our tool.

Did you use the latest version of SpaCET?
SpaCET provides three options to show the visualization region shown below.
If your mentioned "tissue region" is "capture region", imageSize = "CaptureArea" should meet your request.

library(SpaCET)

visiumPath <- file.path(system.file(package = "SpaCET"), "extdata/Visium_BC")
SpaCET_obj <- create.SpaCET.object.10X(visiumPath = visiumPath)
SpaCET_obj <- SpaCET.quality.control(SpaCET_obj, min.genes=100)

# Show the whole image.
SpaCET.visualize.spatialFeature(
    SpaCET_obj, 
    spatialType = "QualityControl", 
    spatialFeatures=c("UMI","Gene"),
    imageBg = TRUE,
    imageSize = "CompleteImage"
)

# Show the capture (or tissue) area.
SpaCET.visualize.spatialFeature(
    SpaCET_obj, 
    spatialType = "QualityControl", 
    spatialFeatures=c("UMI","Gene"),
    imageBg = TRUE,
    imageSize = "CaptureArea"
)

# Show the customized area.
SpaCET.visualize.spatialFeature(
    SpaCET_obj, 
    spatialType = "QualityControl", 
    spatialFeatures=c("UMI","Gene"),
    imageBg = TRUE,
    imageSize = "CustomizedArea",
    CustomizedAreaScale = c(0, 0.2, 0.2, 0.5)
)

Best,
Beibei

[MAXTIAN-BU]

visiumPath <- "D:/II.空间转录组/04. T4/T4"

Create SpaCET object

SpaCET_obj <- create.SpaCET.object.10X(visiumPath = visiumPath)
str(SpaCET_obj)
SpaCET_obj@input$counts[1:8,1:6]
#QC质控：过滤掉表达基因数少于 100 的 spot
SpaCET_obj <- SpaCET.quality.control(SpaCET_obj, min.genes=100)

plot the QC metrics

SpaCET.visualize.spatialFeature(
SpaCET_obj,
spatialType = "QualityControl",
spatialFeatures=c("UMI","Gene"),
imageBg = TRUE,
imageSize = "CompleteImage"
)

[beibeiru]

According to your figure, it's like SpaCET read all sopts to SpaCET_obj.
It's very strange. Do you mind sharing your T4 sample with me?

Best,
Beibei

[beibeiru]

I can not access the file you uploaded previously.

[MAXTIAN-BU]

Already uploaded

[beibeiru]

Hi, @MAXTIAN-BU

Usually, the "filtered_feature_bc_matrix" folder includes only spots covered by tissue.
However, it is weird that your data contains all 5000 spots.

I have added a more filtering step in my package to deal with it!
Please reinstall SpaCET.

# uninstall old version
remove.packages("SpaCET")

# install new version
devtools::install_github("data2intelligence/SpaCET")

library(SpaCET)
visiumPath <- "/Users/rub2/Downloads/T4"
SpaCET_obj <- create.SpaCET.object.10X(visiumPath = visiumPath)
SpaCET_obj <- SpaCET.quality.control(SpaCET_obj, min.genes=100)

SpaCET.visualize.spatialFeature(
    SpaCET_obj, 
    spatialType = "QualityControl", 
    spatialFeatures=c("UMI","Gene"),
    imageBg = TRUE,
    imageSize = "CaptureArea"
)

Best,
Beibei

[MAXTIAN-BU]

Sorry to bother you — after updating the R package, some spots were excessively filtered out.

[beibeiru]

No worries. Feel free to let me know if you have any further questions!

Best,
Beibei