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jfnavarro / st_viewer

A GUI tool for easy and smooth visualisation and analysis of Spatial Transcriptomics datasets
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Normalizing gene signatures #37

Closed lima1 closed 4 years ago

lima1 commented 5 years ago

Hi,

I have some trouble visualizing gene signatures. Without normalization, some of the more subtle differences are obviously lost due to differences in total transcripts per spot. If I turn on normalization, it seems like the normalization uses only on the selected genes, not all, right?

What are the best practices to visualize heatmaps of signatures?

As a related note, I tried to calculate these heatmaps in R with Seurat and generating a spot color file, but it seems like hex color codes are not supported. Would be a nice and useful addition.

I'm still using 0.7.0, so apologies in advance if some of this is changed in newer versions.

Thanks, Markus

jfnavarro commented 4 years ago

I am sorry I completely missed this.

lima1 commented 4 years ago

No worries! Seurat is now supporting spatial data as you know, so I'm all set.