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update sc_dim and sc_violin #20

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merged 3 commits into from
Mar 28, 2024
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  • check the default mapping in sc_dim and sc_violin
> library(scuttle)
> library(scater)
> library(scran)
> library(ggplot2)
> library(ggsc)
> sce <- mockSCE()
> sce <- logNormCounts(sce)
> clusters <- clusterCells(sce, assay.type = 'logcounts')
> colLabels(sce) <- clusters
> sce <- runUMAP(sce, assay.type = 'logcounts')
> set.seed(123)
> genes <- rownames(sce) |> sample(6)
> sc_violin(sce, genes[1], slot = 'logcounts')

image

> sc_violin(sce, genes[1], slot = 'logcounts',
       .fun=function(d) dplyr::filter(d, value > 0)
       ) +
       ggforce::geom_sina(size=.1)

image

sc_violin(sce, genes, slot='logcounts', mapping=aes(x = Cell_Cycle, fill = Cell_Cycle))

abbf6db687bc491ef4d611bbf2409cb

sc_violin(sce, genes, slot='logcounts', mapping=aes(fill = Cell_Cycle))

80ef776a8f2d633eeaa47937c87cc5e

@GuangchuangYu GuangchuangYu merged commit adb85b4 into YuLab-SMU:devel Mar 28, 2024
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