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Samuel Marsh Ph.D.

@samuelmarsh.bsky.social

1.8K followers 859 following 51 posts

Postdoc Beth Stevens Lab | Interested in Alzheimer’s disease, all things single cell, and neuroimmune | Dad 👧👶🏻 | #scicomm #rstats | NEU ‘10 & UCI ’16 samuel-marsh.science

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Samuel Marsh Ph.D. @samuelmarsh.bsky.social · 06/12/2024

scCustomize now includes `seq_zeros` function to easily create sequences with preceding zeros. You can either specify the number of preceding zeros desired or the function will set automatically based on sequence length. 17/n

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Samuel Marsh Ph.D. @samuelmarsh.bsky.social · 06/12/2024

Now here’s two functions that aren’t limited to scRNA-seq analysis but can generally be helpful in your work in R. First, `Split_Vector` which allows you to split a vector in a specified number of chunks or chunks of specific length. 15/n

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Samuel Marsh Ph.D. @samuelmarsh.bsky.social · 06/12/2024

Now we supply that to `cells` parameter of `DoHeatmap` and the result now looks like this. We can now clearly visualize the differences in expression between the identities. To make it even easier you can also just call `Random_Cells_Downsample` from within the `DoHeatmap` call. 14/n

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Samuel Marsh Ph.D. @samuelmarsh.bsky.social · 06/12/2024

However, by using `Random_Cells_Downsample` we can create a plot with equal number of cells per identity for proper visualization. Here I create a down sampled cell vector of 150 cells per group (or the max number of cells for groups smaller than 150 cells) 13/n

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Samuel Marsh Ph.D. @samuelmarsh.bsky.social · 06/12/2024

The default cell level heatmap scales the size of each identity based on the number of cells. This can lead to heatmaps where visualizing the expression in small clusters can be nearly impossible. 12/n

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Samuel Marsh Ph.D. @samuelmarsh.bsky.social · 06/12/2024

The last scCustomize update brought the advance of `Updated_HGNC_Symbols` for updating human gene symbols. This update brings the equivalent function of mice using MGI database: `Updated_MGI_Symbols`. 9/n

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Samuel Marsh Ph.D. @samuelmarsh.bsky.social · 06/12/2024

First, QC functions. `Add_Cell_QC_Metrics` now includes addition of % of hemoglobin counts as metric & chicken was added to default species. Default species are now human, mouse, rat, drosophila, zebrafish, macaque, marmoset, & chicken. One line will add all QC metrics to your object. 2/n

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Samuel Marsh Ph.D. @samuelmarsh.bsky.social · 15/11/2023

Two entirely new plotting functions have been added in v2.0.0: - `QC_Histogram` to plot QC features (or any other meta data or feature/gene) - `FeatureScatter_scCustom` joins the scCustomize family of customized Seurat plots 6/n

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Samuel Marsh Ph.D. @samuelmarsh.bsky.social · 15/11/2023

Some new nice new plotting parameters: - Adding boxplots to any violin plot function with `plot_boxplot` - Just add median with `plot_median` - Removing plot axes in any DimPlot-based function with `figure_plot` 5/n

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Samuel Marsh Ph.D. @samuelmarsh.bsky.social · 15/11/2023

Ok, now for the good stuff! V2.0.0 adds a number of new QC metrics (see reorganized vignette here for details: samuel-marsh.github.io/scCustomize/... v2.0.0 also introduces a one-liner to add all qc metrics in one fell swoop: 4/n

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