Description Usage Arguments Value
View source: R/plotting_ident.R
Graphs the output of a dimensional reduction technique (PCA by default).
Based on Seurat::DimPlot
.
Cells are colored by their identity class. This identity class object@ident
should be set prior to running this code. See ClusterCellsKmeans
and EvaluateIdentKmeans
.
1 2 3 4 5 6 7 8 9 10 11 | DimPlot2(object, reduction.use = "pca", ident.threshold = 0.9,
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", ...)
|
object |
Seurat object |
reduction.use |
Which dimensionality reduction to use. Default is "pca", can also be "tsne", or "ica", assuming these are precomputed. |
ident.threshold |
A probability threshold for cell identities,
using |
dim.1 |
Dimension for x-axis (default 1) |
dim.2 |
Dimension for y-axis (default 2) |
cells.use |
Vector of cells to plot (default is all cells) |
pt.size |
Adjust point size for plotting |
do.return |
Return a ggplot2 object (default : FALSE) |
do.bare |
Do only minimal formatting (default : FALSE) |
cols.use |
Vector of colors, each color corresponds to an identity class. By default, ggplot assigns colors. |
group.by |
Group (color) cells in different ways (for example, orig.ident) |
pt.shape |
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. |
do.hover |
Enable hovering over points to view information |
data.hover |
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. |
do.identify |
Opens a locator session to identify clusters of cells. |
do.label |
Whether to label the clusters |
label.size |
Sets size of labels |
no.legend |
Setting to TRUE will remove the legend |
coord.fixed |
Use a fixed scale coordinate system (for spatial coordinates). Default is FALSE. |
no.axes |
Setting to TRUE will remove the axes |
dark.theme |
Use a dark theme for the plot |
plot.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). |
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 |
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 |
plot.title |
Title for plot |
vector.friendly |
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. |
png.file |
Used only if vector.friendly is TRUE. Location for temporary PNG file. |
png.arguments |
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) |
na.value |
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.
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