Returns a DimPlot colored based on whether the cells fall in clusters to the left or to the right of a node split in the cluster tree.
ColorDimSplit(
object,
node,
left.color = "red",
right.color = "blue",
other.color = "grey50",
...
)
Returns a DimPlot
Seurat object
Node in cluster tree on which to base the split
Color for the left side of the split
Color for the right side of the split
Color for all other cells
Arguments passed on to DimPlot
dims
Dimensions to plot, must be a two-length numeric vector specifying x- and y-dimensions
cells
Vector of cells to plot (default is all cells)
cols
Vector of colors, each color corresponds to an identity class. This may also be a single character
or numeric value corresponding to a palette as specified by brewer.pal.info
.
By default, ggplot2 assigns colors. We also include a number of palettes from the pals package.
See DiscretePalette
for details.
pt.size
Adjust point size for plotting
reduction
Which dimensionality reduction to use. If not specified, first searches for umap, then tsne, then pca
group.by
Name of one or more metadata columns to group (color) cells by (for example, orig.ident); pass 'ident' to group by identity class
split.by
A factor in object metadata to split the plot by, pass 'ident' to split by cell identity'
shape.by
If NULL, all points are circles (default). You can specify any
cell attribute (that can be pulled with FetchData) allowing for both
different colors and different shapes on cells. Only applicable if raster = FALSE
.
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)
shuffle
Whether to randomly shuffle the order of points. This can be useful for crowded plots if points of interest are being buried. (default is FALSE)
seed
Sets the seed if randomly shuffling the order of points.
label
Whether to label the clusters
label.size
Sets size of labels
label.color
Sets the color of the label text
label.box
Whether to put a box around the label text (geom_text vs geom_label)
alpha
Alpha value for plotting (default is 1)
repel
Repel labels
cells.highlight
A list of character or numeric vectors of cells to
highlight. If only one group of cells desired, can simply
pass a vector instead of a list. If set, colors selected cells to the color(s)
in cols.highlight
and other cells black (white if dark.theme = TRUE);
will also resize to the size(s) passed to sizes.highlight
cols.highlight
A vector of colors to highlight the cells as; will repeat to the length groups in cells.highlight
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.
na.value
Color value for NA points when using custom scale
ncol
Number of columns for display when combining plots
combine
Combine plots into a single patchworked
ggplot object. If FALSE
, return a list of ggplot objects
raster
Convert points to raster format, default is NULL
which
automatically rasterizes if plotting more than 100,000 cells
raster.dpi
Pixel resolution for rasterized plots, passed to geom_scattermore(). Default is c(512, 512).
DimPlot
if (FALSE) {
if (requireNamespace("ape", quietly = TRUE)) {
data("pbmc_small")
pbmc_small <- BuildClusterTree(object = pbmc_small, verbose = FALSE)
PlotClusterTree(pbmc_small)
ColorDimSplit(pbmc_small, node = 5)
}
}
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