Comments (3)
Hi @laleaton,
I performed a quick implementation of the Z-scoring on a gene-basis in do_DotPlot()
. This allows to set the distribution of the Avg. Expression of a given gene across the groups so that the mean is 0 and standard deviation is 1. This allows you to quickly check which group/s have the highest avg. expression values for a given gene, but you should then avoid performing gene-wise comparisons.
This said:
- Use
scale.data = TRUE
to access this functionality. It will not work withslot = "scale.data"
. - You would want also to play around with
max.cutoff
andmin.cutoff
to set the color scale right. - This behaviour is inherently different from the one provided in
Seurat
. Please be aware of that.
You can access this under the latest commit. Please be aware that you are again downloading the most recent and potentially buggy version of the pacakge!
devtools::install_github("enblacar/SCpubr", ref = "af2828dbfce7a11562a0f6d3fc447122fbf66670")
Hope this helps!
Enrique
from scpubr.
Hi @laleaton,
Thanks for using my package!
Please keep in mind that you downloaded theHEAD
commit of the R package. This means that you are just currently using the R package as I am right now as the developer, it all its beauty and "bugginess" ahhahaha If you ever consider downloading the "development" versions of the package, always refer to the official Releases, which I incorporate with every CRAN update.
This said, for the next CRAN version I have refactored the SCpubr::do_DotPlot()
function entirely, removing the dependency with Seurat::DotPlot()
. This means I am no longer using the native function from Seurat
as the basis of the plot, but rather generating my own version of the dot plot. This also means that I am no longer using the scale
parameter, as this was using the Seurat
's scaling implementation. I have on my to-do list to allow for z-scoring of the values, if desired, but this is yet to be implemented. It will definitely roll out on the next CRAN update, though. Yet, this might not end up being exactly the same as with Seurat
.
I can give you a heads up when I implement it, if you want! For the time being, please revert to the CRAN version if you want to still use the scale
parameter.
I hope this was helpful!
Enrique
from scpubr.
Thank you Enrique! Yes, please do let me know when you implement scaling. I really appreciate your prompt and thorough response!
Cheers,
Laura Ann
from scpubr.
Related Issues (20)
- Extract coordinated from do_CellularStatesPlot HOT 2
- ncol | do_DimPlot | ncol argument scaling combined plot differently to other plots HOT 3
- REQUEST | do_DimPlot | Create UMAP with Table HOT 1
- REQUEST | do_DotPlot | Allow duplicated features HOT 1
- BUG | do_FeaturePlot | diverging.palette argument is not working HOT 8
- BUG | do_VolcanoPlot | add gene tags based on logFC + pvalue HOT 1
- REQUEST | do_DotPlot | Reqeuest for the option "dot.min". HOT 1
- How to create custom mappings from p-values to annotation for BoxPlot HOT 1
- Show Genenames in featureplot for feature vector HOT 5
- Fix typo | do_ViolinPlot | Spelling Error HOT 1
- BUG | do_FeaturePlot | The legend titles are not displayed anymore HOT 7
- Seurat v5 Support HOT 3
- REQUEST | doDimPlot | Plot NA values of grouping values in background HOT 1
- Violin Feature Plots HOT 2
- REQUEST | do_FeaturePlot | Is it possible to have one feature plot with multiple genes? HOT 3
- label.font only works for legend but not for labels shown on umap HOT 4
- REQUEST | subgroups in dotplot HOT 3
- REQUEST | do_RidgePlot | Extending Data Lines
- No do_LigandReceptorPlot HOT 2
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from scpubr.