NNPlot: Highlight Neighbors in DimPlot

In satijalab/seurat: Tools for Single Cell Genomics

Highlight Neighbors in DimPlot

Description

It will color the query cells and the neighbors of the query cells in the DimPlot

Usage

NNPlot(
  object,
  reduction,
  nn.idx,
  query.cells,
  dims = 1:2,
  label = FALSE,
  label.size = 4,
  repel = FALSE,
  sizes.highlight = 2,
  pt.size = 1,
  cols.highlight = c("#377eb8", "#e41a1c"),
  na.value = "#bdbdbd",
  order = c("self", "neighbors", "other"),
  show.all.cells = TRUE,
  ...
)

Arguments

object	Seurat object
reduction	Which dimensionality reduction to use. If not specified, first searches for umap, then tsne, then pca
nn.idx	the neighbor index of all cells
query.cells	cells used to find their neighbors
dims	Dimensions to plot, must be a two-length numeric vector specifying x- and y-dimensions
label	Whether to label the clusters
label.size	Sets size of labels
repel	Repel labels
sizes.highlight	Size of highlighted cells; will repeat to the length groups in cells.highlight. If sizes.highlight = TRUE size of all points will be this value.
pt.size	Adjust point size for plotting
cols.highlight	A vector of colors to highlight the cells as; will repeat to the length groups in cells.highlight
na.value	Color value for NA points when using custom scale
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)
show.all.cells	Show all cells or only query and neighbor cells
...	Extra parameters passed to DimPlot

Value

A patchworked ggplot object if combine = TRUE; otherwise, a list of ggplot objects

satijalab/seurat documentation built on May 11, 2024, 4:04 a.m.