plotSpatial2D | R Documentation |
Visualize a spatial dataset
Description
Simple visualization of spatial coordinates. See example code for how to have
information preset in the object. Arguments to the liger object method are
passed down to ligerDataset method.
Usage
plotSpatial2D(object, ...)
## S3 method for class 'liger'
plotSpatial2D(object, dataset, useCluster = NULL, legendColorTitle = NULL, ...)
## S3 method for class 'ligerSpatialDataset'
plotSpatial2D(
object,
useCluster = NULL,
legendColorTitle = NULL,
useDims = c(1, 2),
xlab = NULL,
ylab = NULL,
labelText = FALSE,
panelBorder = TRUE,
...
)
Arguments
object |
Either a liger object containing a spatial
dataset or a ligerSpatialDataset object.
|
... |
Arguments passed on to .ggScatter , .ggplotLigerTheme
dotOrder Controls the order that each dot is added to the plot. Choose
from "shuffle" , "ascending" , or "descending" . Default
"shuffle" , useful when coloring by categories that overlaps (e.g.
"dataset"), "ascending" can be useful when coloring by a continuous
variable (e.g. gene expression) where high values needs more
highlight. NULL use default order.
dotSize,dotAlpha Numeric, controls the size or transparency of all
dots. Default getOption("ligerDotSize") (1) and 0.9 .
raster Logical, whether to rasterize the plot. Default NULL
automatically rasterize the plot when number of total dots to be plotted
exceeds 100,000.
labelTextSize Numeric, controls the size of label size when
labelText = TRUE . Default 4 .
seed Random seed for reproducibility. Default 1 .
showLegend Whether to show the legend. Default TRUE .
legendPosition Text indicating where to place the legend. Choose from
"top" , "bottom" , "left" or "right" . Default
"right" .
baseSize One-parameter control of all text sizes. Individual text
element sizes can be controlled by other size arguments. "Title" sizes are
2 points larger than "text" sizes when being controlled by this.
titleSize,xTitleSize,yTitleSize,legendTitleSize Size of main title,
axis titles and legend title. Default NULL controls by
baseSize + 2 .
subtitleSize,xTextSize,yTextSize,legendTextSize Size of subtitle text,
axis texts and legend text. Default NULL controls by baseSize .
legendDotSize Allow dots in legend region to be large enough to see
the colors/shapes clearly. Default 4 .
colorLabels Character vector for modifying category names in a
color legend. Passed to ggplot2::scale_color_manual(labels) . Default
NULL uses original levels of the factor.
colorValues Character vector of colors for modifying category colors
in a color legend. Passed to ggplot2::scale_color_manual(values) .
Default NULL uses internal selected palette when <= 26 categories are
presented, otherwise ggplot hues.
legendNRow,legendNCol Integer, when too many categories in one
variable, arranges number of rows or columns. Default NULL ,
automatically split to ceiling(levels(variable)/15) columns.
naColor The color code for NA values. Default "#DEDEDE" .
scale_colour_gradient2 . Default NULL .
|
dataset |
Name of one spatial dataset.
|
useCluster |
Either the name of one variable in cellMeta(object)
or a factor object with annotation that matches with all cells in the
specified dataset. Default NULL uses default clusters.
|
legendColorTitle |
Alternative title text in the legend. Default
NULL uses the variable name set by useCluster , or
"Annotation" is useCluster is a customized factor object.
|
useDims |
Numeric vector of two, choosing the coordinates to be drawn
on 2D space. (STARmap data could have 3 dimensions.) Default c(1, 2) .
|
xlab , ylab |
Text label on x-/y-axis. Default NULL does not show
it.
|
labelText |
Logical, whether to label annotation onto the scatter plot.
Default FALSE .
|
panelBorder |
Whether to show rectangle border of the panel instead of
using ggplot classic bottom and left axis lines. Default TRUE .
|
Value
A ggplot object
Examples
ctrl.fake.spatial <- as.ligerDataset(dataset(pbmc, "ctrl"), modal = "spatial")
fake.coords <- matrix(rnorm(2 * ncol(ctrl.fake.spatial)), ncol = 2)
coordinate(ctrl.fake.spatial) <- fake.coords
dataset(pbmc, "ctrl") <- ctrl.fake.spatial
defaultCluster(pbmc) <- pbmcPlot$leiden_cluster
plotSpatial2D(pbmc, dataset = "ctrl")