Seurat (version 3.1.1)

ColorDimSplit: Color dimensional reduction plot by tree split

Description

Returns a DimPlot colored based on whether the cells fall in clusters to the left or to the right of a node split in the cluster tree.

Usage

ColorDimSplit(object, node, left.color = "red", right.color = "blue",
  other.color = "grey50", ...)

Arguments

object

Seurat object

node

Node in cluster tree on which to base the split

left.color

Color for the left side of the split

right.color

Color for the right side of the split

other.color

Color for all other cells

...

Arguments passed on to DimPlot

dims

Dimensions to plot, must be a two-length numeric vector specifying x- and y-dimensions

cells

Vector of cells to plot (default is all cells)

cols

Vector of colors, each color corresponds to an identity class. This may also be a single character or numeric value corresponding to a palette as specified by brewer.pal.info. By default, ggplot2 assigns colors

pt.size

Adjust point size for plotting

reduction

Which dimensionality reduction to use. If not specified, first searches for umap, then tsne, then pca

group.by

Name of one or more metadata columns to group (color) cells by (for example, orig.ident); pass 'ident' to group by identity class

split.by

Name of a metadata column to split plot by; see FetchData for more details

shape.by

If NULL, all points are circles (default). You can specify any cell attribute (that can be pulled with FetchData) allowing for both different colors and different shapes on cells

order

Specify the order of plotting for the idents. This can be useful for crowded plots if points of interest are being buried. Provide either a full list of valid idents or a subset to be plotted last (on top)

label

Whether to label the clusters

label.size

Sets size of labels

repel

Repel labels

cells.highlight

A list of character or numeric vectors of cells to highlight. If only one group of cells desired, can simply pass a vector instead of a list. If set, colors selected cells to the color(s) in cols.highlight and other cells black (white if dark.theme = TRUE); will also resize to the size(s) passed to sizes.highlight

cols.highlight

A vector of colors to highlight the cells as; will repeat to the length groups in cells.highlight

sizes.highlight

Size of highlighted cells; will repeat to the length groups in cells.highlight

na.value

Color value for NA points when using custom scale

combine

Combine plots into a single gg object; note that if TRUE; themeing will not work when plotting multiple features

ncol

Number of columns for display when combining plots

Value

Returns a DimPlot

Examples

# NOT RUN {
pbmc_small
pbmc_small <- BuildClusterTree(object = pbmc_small, verbose = FALSE)
PlotClusterTree(pbmc_small)
ColorDimSplit(pbmc_small, node = 5)

# }