NNPlot {Seurat}

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