plot_gene_exprs: Plot gene expression in cells
In jacobheng/cellwrangler: Supplemental toolkit for single-cell RNAseq analysis

Description Usage Arguments Value Examples

plot_gene_exprs() plots levels of expression of a specified gene or genes as a color gradient. A two-dimensional dimensionality reduction object with coordinates for each cell (e.g. by t-SNE or UMAP dimensionality reduction) is required.

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plot_gene_exprs(cds, genes, dim_reduction, color_scale = c("slategray1",
  "red"), limits = c(0, 10), rescale = F, cell_size = 0.1,
  group_vector = NULL, group_facet = NULL, title = NULL)

`cds`	a CellDataSet object or equivalent
`genes`	a vector of gene name(s) to plot
`dim_reduction`	a dataframe specifying the coordinates of a dimensionality reduction output (e.g. t-SNE, UMAP etc.). Each column should specify one dimension.
`color_scale`	a vector of two colors for color gradient
`limits`	a vector containing two number specifying the lower and upper limits of the color scale respectively.
`rescale`	logical; whether to rescale color scale as a continuous gradient from the minimum to the maximum value of expression for specified gene; defaults to FALSE
`cell_size,`	the size of the point representing each cell
`group_vector`	a vector classifying cells e.g. genotype or condition
`group_facet`	input for facet_grid() argument. A group vector must be supplied
`title`	title of plot

A ggplot2 object

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plot_gene_exprs(myCDS, genes=c("Acta2","Myl9"), dim_reduction=tsne_proj[,c("TSNE.1", "TSNE.2")],
color_scale=c("blue","red"), limits = c(0,5), rescale= TRUE, cell_size =0.1, group_vector=pData(dat)$genotype,
group_facet="group~variable", title=NULL )