scCustomize

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control border thickness of Stacked_VlnPlot

8

Hi @samuel-marsh! Thanks for this useful package. Is there anyway to change the border thickness of `Stacked_VlnPlot`? When I save it with ggsave and arrange it into a figure it...

massonix

Flip clustered dotplot

1

Hello Samuel, Thanks for this package! Is there a way to quickly flip a clustered_DotPlot? Thanks! Francesco

france-hub

Move progress bars to cli framework

1

- [ ] Using `cli_progress_along()` mainly - [ ] Rewrite pblapply functions to match format needed - [ ] Remove old pblapply options - [ ] Remove pbapply dependency

samuel-marsh

Clustered Dotplot

9

- [x] fix percent mat subset when NAs present - [x] Fix expression color selection default - [ ] Domino plot annotation - [x] Add vignette and rebuild

samuel-marsh

- [ ] Custom/Enhanced Seurat Heatmap - [ ] Easy Aesthetic Volcano Plots - [ ] Cell Bender. Easy add to existing object.

samuel-marsh

Added features for `Percent_Expressing`

2

- [ ] Support for setting individual expression thresholds for each feature supplied - [ ] Support for quantifying cells expressing two or more features simultaneously

samuel-marsh

Duplicate cell name error in Cell_Highlight_Plot, even though they are not duplicate

1

Error in `Cell_Highlight_Plot()`: ! The list of `cells_highlight` contains duplicate cell names. ℹ Ensure all cell names are unique before plotting. Run `rlang::last_trace()` to see where the error occurred.

yojetsharma

Adding SpatialPlots

4

Dear Samuel, I really like to use your package. It would be great to use it for spatial data (10x genomics) as well (e.g. SpatialPlot). Best, Nina

nina-hahn

split.by error in Clustered_DotPlot function

3

Hi, Thank you for the package. I was able to use the function Clustered_DotPlot without using split.by parameter. I want to look at the expression at different timepoints and time2...

apal6

Release Prep v2.2.0

3

**To Do:** - [x] anndata warnings (https://github.com/samuel-marsh/scCustomize/issues/162) - [x] LIGER 2.0 compatibility or warning messages (https://github.com/samuel-marsh/scCustomize/issues/161) - [x] Spatial Plots (if time) (https://github.com/samuel-marsh/scCustomize/issues/160) - [x] ~ggprism workaround if not fixed...

samuel-marsh