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b/man/vrSpatialPlot.Rd |
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% Generated by roxygen2: do not edit by hand |
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% Please edit documentation in R/visualization.R |
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\name{vrSpatialPlot} |
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\alias{vrSpatialPlot} |
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\title{vrSpatialPlot} |
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\usage{ |
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vrSpatialPlot( |
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object, |
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group.by = "Sample", |
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plot.segments = FALSE, |
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group.ids = NULL, |
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colors = NULL, |
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n.tile = 0, |
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assay = NULL, |
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graph.name = NULL, |
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graph.edge.color = "orange", |
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reduction = NULL, |
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ncol = 2, |
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nrow = NULL, |
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font.size = 2, |
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pt.size = 2, |
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cell.shape = 21, |
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alpha = 1, |
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label = FALSE, |
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spatial = NULL, |
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channel = NULL, |
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background.color = NULL, |
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background = NULL, |
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reg = FALSE, |
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crop = FALSE, |
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legend.pt.size = 2, |
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legend.text.size = 14, |
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scale.image = TRUE, |
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legend.loc = "right", |
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common.legend = TRUE, |
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collapse.plots = TRUE, |
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interactive = FALSE, |
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shiny.options = list() |
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) |
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} |
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\arguments{ |
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\item{object}{a VoltRon object} |
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\item{group.by}{a column of metadata from \link{Metadata} used as grouping label for the spatial entities} |
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\item{plot.segments}{plot segments from \link{vrSegments} instead of points} |
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\item{group.ids}{a subset of categories defined in metadata column from \code{group.by}} |
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\item{colors}{the color set for group.by. Should be of the same size of group.id (if specified) or unique elements in group.by} |
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\item{n.tile}{should points be aggregated into tiles before visualization (see \link{geom_tile}). Applicable only for cells and molecules} |
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\item{assay}{assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see \link{SampleMetadata}. |
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if NULL, the default assay will be used, see \link{vrMainAssay}.} |
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\item{graph.name}{if not NULL, the spatial graph is with name \code{graph.name} is visualized as well, see \link{vrGraphNames}} |
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\item{graph.edge.color}{the colors of the graph edges, if \code{graph.name} is not NULL.} |
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\item{reduction}{used by \code{vrSpatialPlotVitessce} to visualize an embedding alongside with the spatial plot.} |
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\item{ncol}{column wise number of plots, for \link{ggarrange}} |
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\item{nrow}{row wise number of plots, for \link{ggarrange}} |
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\item{font.size}{font size} |
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\item{pt.size}{point size} |
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\item{cell.shape}{the shape of the points representing cells, see \link{geom_point}} |
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\item{alpha}{alpha level of colors of visualized points and segments} |
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\item{label}{if TRUE, the labels of the ROI assays will be visualized} |
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\item{spatial}{the name of the main spatial system} |
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\item{channel}{the name of the channel associated with the image} |
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\item{background.color}{the color of plot background if a channel is not specified, or the spatial coord system doesnt have an image.} |
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\item{background}{(DEPRECATED) the background of the plot. Either an image name, see \link{vrImageNames} or a vector of length two with image name |
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and a channel name, see \link{vrImageChannelNames}. Type "black" or "white" for black or white backgrounds. if NULL, the main image (\link{vrMainSpatial}) |
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and main channel (\link{vrMainChannel}) will be in the background. Otherwise the background will be grey.} |
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\item{reg}{TRUE if registered coordinates of the main image (\link{vrMainSpatial}) is requested} |
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\item{crop}{whether to crop an image of a spot assay to the extend of spots} |
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\item{legend.pt.size}{the size of points at the legend} |
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\item{legend.text.size}{the size of the text at the legend} |
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\item{scale.image}{if TRUE, background image will be scaled down to a low resolution (width: 1000px)} |
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\item{legend.loc}{the location of the legend, default is "right"} |
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\item{common.legend}{whether to use a common legend for all plots, see \link{ggarrange}} |
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\item{collapse.plots}{whether to combine all ggplots} |
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\item{interactive}{if TRUE, run interactive plot} |
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\item{shiny.options}{a list of shiny options (browser, host, port etc.) passed \code{options} arguement of \link{shinyApp}. For more information, see \link{runApp}} |
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} |
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\description{ |
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Plotting identification of spatially resolved cells, spots, and ROI on associated images from multiple assays in a VoltRon object. |
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} |