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bhuvad / SpaNorm

R package for normalisation of spatial transcriptomics data
https://bhuvad.github.io/SpaNorm/
GNU General Public License v3.0
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plotGeneExpression function not found #5

Closed swaruplab closed 3 months ago

swaruplab commented 3 months ago

When plotting gene-expression using the GitHub tutorial, function plotGeneExpression is not defined and I could not find it in the GitHub code. Please help.

swaruplab commented 3 months ago 
HumanDLPFC = [SpaNorm](https://bhuvad.github.io/SpaNorm/reference/SpaNorm.html)(HumanDLPFC, adj.method = "pearson")
p_pearson = plotGeneExpression(HumanDLPFC, "MOBP") +
  [ggtitle](https://ggplot2.tidyverse.org/reference/labs.html)("Pearson")
bhuvad commented 3 months ago

Hi @swaruplab,

The plotting function we have in the vignette is just for demonstration purposes. It is not implemented as part of the package and is not dynamic enough to handle all possible use cases. You can find the source code for that in the vignette markdown document: https://github.com/bhuvad/SpaNorm/blob/de33b2d5357fa0bda20022c2dc9344cbde009734/vignettes/SpaNorm.Rmd#L47

I have plans to implement a more generic plotting function and will push that later in the year. It is mostly ready but needs the final polishing touches. We aim to have it ready by the next bioconductor release that should be in a couple of months.

Cheers, Dharmesh