MultiFeaturePlot: Plotting Multiple Features on a Dimensionality Reduced Space
In chenyenchung/PlotSeurat: Plots That You Might Also Want With Seurat

Description Usage Arguments Details Value

MultiFeaturePlot() plots cells in a Seurat object into a t-SNE space or other dimensionality reduced space for visualization. Each point will be colored according to log-normalized expression level (from @data slot of a Seurat object). The first gene will be colored in red, the second gene will be colored in green, and the third gene will be colored in blue.

1 2	MultiFeaturePlot(object, features, assay = "RNA", pt.size = 1, reduction = "tsne", cells.use = NULL, title = NULL)

`object`	a Seurat object (v2 or v3)
`features`	a character vector of features to plot
`assay`	a character string indicating the assay to plot (SeuratV3 only)
`pt.size`	a number indicating the size of points on the plot
`reduction`	a character string indicating the reduction to embed the cells on the plot (e.g., "tsne" or "pca")
`cells.use`	a character vector of cell names indicating the cells to include in the plot (try `WhichCells()`)
`title`	a character string for customized plot title. If not set, the default is the feature names

Specifically, the gene expression is translated into color by first taking the full range of expression from zero to highest, binning them into 256 bins, and use the binned expression level as 8-bit color code.

a ggplot object

chenyenchung/PlotSeurat documentation built on May 21, 2019, 11:40 a.m.