NNPlot: 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,
  ...
)

Value

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

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