Visualize a spatial dataset — plotSpatial2D • rliger

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 liger
plotSpatial2D(object, dataset, useCluster = NULL, legendColorTitle = NULL, ...)

# S3 method for 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)/10) 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
#> ! No rownames with given spatial coordinate. Assuming they match with the cells.
#> ! No colnames with given spatial coordinate. Setting to "x" and "y"
dataset(pbmc, "ctrl") <- ctrl.fake.spatial
#> ℹ Updated QC variables: "nUMI" and "nGene"
defaultCluster(pbmc) <- pbmcPlot$leiden_cluster
#> ℹ Storing given cluster labels to `cellMeta(x)` field: "defaultCluster".
plotSpatial2D(pbmc, dataset = "ctrl")