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Hi I was wondering why the `imgData` slot of a `SpatialExperiment` restricts to columns
‘sample_id’, ‘image_id’, ‘data’, ‘scaleFactor’
I can imagine many scenarios where one would might want to …
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Discussed in #76, but someone must have introduced a regression somewhere down the line.
These lines of code:
https://github.com/drighelli/SpatialExperiment/blob/fbc21539ad3b8ec73c167b7bf4fff798…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/estellad/SpatialExperimentIO
Confirm the followin…
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For doing clustering with `spatialCluster()`, the vignette makes it clear that `colData()` must have columns named "row" and "col" (#34, #40). When calling `spatialEnhance() `with visium, it now expec…
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Hi - I was just trying out `ggspavis` and was wondering about possibilities for increasing the point size (for the spots) in the output from the `plotVisium` function. The plots look fine e.g. in the …
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Dear Edward,
I am trying to run bayes space version ‘1.8.2’ with visium ST data (from Cytassist). When I run
spatialCluster(se_filtered, q=8, platform="Visium", d=7, nit.method="mclust", model="…
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Hello,
I ran escape using the following code but encountered errors that I cannot resolve:
library(escape)
H
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Hi Marcel,
Some of the TENxVisiumData package miss the "spatial coordinates" bit of information because this was formerly stored in a file called `tissue_positions_list.csv` (see [here](https://www…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/phipsonlab/jazzPanda
Confirm the following by edi…
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I have successfully visualized individual tissue samples with a standard output structure using `SpatialFeaturePlot`, but I would like to visualize multiple samples in one of Spaceranger's _aggregated…