Seurat (version 2.1.0)

DotPlotOld: Old Dot plot visualization (pre-ggplot implementation) Intuitive way of visualizing how gene expression changes across different identity classes (clusters). The size of the dot encodes the percentage of cells within a class, while the color encodes the AverageExpression level of 'expressing' cells (green is high).

Description

Old Dot plot visualization (pre-ggplot implementation) Intuitive way of visualizing how gene expression changes across different identity classes (clusters). The size of the dot encodes the percentage of cells within a class, while the color encodes the AverageExpression level of 'expressing' cells (green is high).

Usage

DotPlotOld(object, genes.plot, cex.use = 2, cols.use = NULL,
  thresh.col = 2.5, dot.min = 0.05, group.by = NULL)

Arguments

object

Seurat object

genes.plot

Input vector of genes

cex.use

Scaling factor for the dots (scales all dot sizes)

cols.use

colors to plot

thresh.col

The raw data value which corresponds to a red dot (lowest expression)

dot.min

The fraction of cells at which to draw the smallest dot (default is 0.05)

group.by

Factor to group the cells by

Value

Only graphical output

Examples

# NOT RUN {
cd_genes <- c("CD247", "CD3E", "CD9")
DotPlotOld(object = pbmc_small, genes.plot = cd_genes)

# }