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