Graphs the output of a dimensional reduction technique (PCA by default). Cells are colored by their identity class.
DimPlot(object, reduction.use = "pca", dim.1 = 1, dim.2 = 2,
cells.use = NULL, pt.size = 1, do.return = FALSE, do.bare = FALSE,
cols.use = NULL, group.by = "ident", pt.shape = NULL,
do.hover = FALSE, data.hover = "ident", do.identify = FALSE,
do.label = FALSE, label.size = 4, no.legend = FALSE,
coord.fixed = FALSE, no.axes = FALSE, dark.theme = FALSE,
plot.order = NULL, cells.highlight = NULL, cols.highlight = "red",
sizes.highlight = 1, plot.title = NULL, vector.friendly = FALSE,
png.file = NULL, png.arguments = c(10, 10, 100), na.value = "grey50",
...)Seurat object
Which dimensionality reduction to use. Default is "pca", can also be "tsne", or "ica", assuming these are precomputed.
Dimension for x-axis (default 1)
Dimension for y-axis (default 2)
Vector of cells to plot (default is all cells)
Adjust point size for plotting
Return a ggplot2 object (default : FALSE)
Do only minimal formatting (default : FALSE)
Vector of colors, each color corresponds to an identity class. By default, ggplot assigns colors.
Group (color) cells in different ways (for example, orig.ident)
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.
Enable hovering over points to view information
Data to add to the hover, pass a character vector of features to add. Defaults to cell name and ident. Pass 'NULL' to clear extra information.
Opens a locator session to identify clusters of cells.
Whether to label the clusters
Sets size of labels
Setting to TRUE will remove the legend
Use a fixed scale coordinate system (for spatial coordinates). Default is FALSE.
Setting to TRUE will remove the axes
Use a dark theme for the plot
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).
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
A vector of colors to highlight the cells as; will repeat to the length groups in cells.highlight
Size of highlighted cells; will repeat to the length groups in cells.highlight
Title for plot
FALSE by default. If TRUE, points are flattened into a PNG, while axes/labels retain full vector resolution. Useful for producing AI-friendly plots with large numbers of cells.
Used only if vector.friendly is TRUE. Location for temporary PNG file.
Used only if vector.friendly is TRUE. Vector of three elements (PNG width, PNG height, PNG DPI) to be used for temporary PNG. Default is c(10,10,100)
Color value for NA points when using custom scale.
Extra parameters to FeatureLocator for do.identify = TRUE
If do.return==TRUE, returns a ggplot2 object. Otherwise, only graphical output.
FeatureLocator
# NOT RUN {
DimPlot(object = pbmc_small)
# }
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