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b/man/vrSpatialFeaturePlot.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{vrSpatialFeaturePlot} |
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\alias{vrSpatialFeaturePlot} |
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\title{vrSpatialFeaturePlot} |
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\usage{ |
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vrSpatialFeaturePlot( |
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object, |
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features, |
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combine.features = FALSE, |
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group.by = "label", |
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plot.segments = FALSE, |
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n.tile = 0, |
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norm = TRUE, |
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log = FALSE, |
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assay = NULL, |
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graph.name = 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 = 16, |
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title.size = 10, |
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alpha = 0.6, |
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keep.scale = "feature", |
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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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scale.image = TRUE, |
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common.legend = FALSE, |
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legend.loc = "right", |
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collapse.plots = TRUE |
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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{features}{a set of features to be visualized, either from \link{vrFeatures} of raw or normalized data or columns of the \link{Metadata}.} |
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\item{combine.features}{whether to combine all features in one plot} |
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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{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{norm}{if TRUE, the normalized data is used} |
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\item{log}{if TRUE, data features (excluding metadata features) will be log transformed} |
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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{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{title.size}{title size of legend and plot} |
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\item{alpha}{alpha level of colors of visualized points and segments} |
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\item{keep.scale}{whether unify all scales for all features or not} |
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\item{label}{if TRUE, labels of ROIs will be visualized too} |
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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{scale.image}{if TRUE, background image will be scaled down to a low resolution (width: 1000px)} |
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\item{common.legend}{whether to use a common legend for all plots, see \link{ggarrange}} |
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\item{legend.loc}{the location of the legend, default is "right"} |
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\item{collapse.plots}{whether to combine all ggplots} |
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} |
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\description{ |
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Plotting single/multiple features of spatially resolved cells, spots, and ROI on associated images from multiple assays in a VoltRon object. |
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} |