Highlight Neighbors in DimPlot
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,
...
)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 |
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 |
A patchworked ggplot object if
combine = TRUE; otherwise, a list of ggplot objects
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