STPlot: Graphs ST spots colored by continuous or categorical features

In jbergenstrahle/STUtility: Analysis and visualization of Spatial Transcriptomics data

Graphs ST spots colored by continuous or categorical features

Description

Graphs ST spots colored by continuous or categorical features

Usage

STPlot(
  data,
  data.type = NULL,
  variable,
  pt.size = 1,
  pt.alpha = 1,
  pt.border = FALSE,
  palette = "MaYl",
  cols = NULL,
  ncol = NULL,
  spot.colors = NULL,
  center.zero = TRUE,
  center.tissue = FALSE,
  plot.title = NULL,
  dims = NULL,
  split.labels = FALSE,
  pxum = NULL,
  sb.size = 2.5,
  dark.theme = FALSE,
  limits = NULL,
  label.by = NULL,
  ...
)

Arguments

data	Object of class 'data.frame' containing at least (x, y) coordinates, a "sample" vector with labels for each sample and one column with the feature values. Can also include an additional column for shapes.
data.type	String specifying the class of the features in data to be plotted
variable	Name of feature column
pt.size	Point size of each ST spot [default: 1]
pt.alpha	Opacity of each ST spot [default: 1]
pt.border	Should a border be drawn around the spots? [default: TRUE]
palette	Color palette used for spatial heatmap (see palette.select(info = T) for available options). Disabled if a color vector is provided (see cols below).
cols	A vector of colors to use for colorscale, e.g. cols = c("blue", "white", "red") will create a gradient color scale going from blue to white to red. This options will deactivate the palette option.
ncol	Number of columns to arrange the samples into. This can for example be useful to adjust if you want to visualize the samples in just in one row or one column.
spot.colors	Character vector with color names that overrides default coloring with ggplot2
center.zero	Specifies whther or not the colorscale should be centered around 0. For some values, such as Principal Component vectors, the distribution of values is centered at 0 and in that case it can be appropriate to use a divergent colorscale with a predefined value for 0. If this parameter is set to TRUE, the ggplot2 function scale_color_gradient2 will be used to control the coloring instead of scale_color_gradientn. If center.zero is set to FALSE, the colorscale will simply map the values in equally spaced intervals which could skew the interpretaion of the output plot.
center.tissue	Adjust coordinates so that the center of the tissue is in the middle of the array along the y-axis. This can be useful if your samples have been placed in very different parts of the capture area and you want to center the plots in the middle. This is however unnecessary if you have already aligned the sample data (see AlignImages, WarpImages and ManualAlignImages)
plot.title	String specifying the title of the plot
dims	List of dimensions for x and y scales. If you have mixed datasets from different arrays (platforms) with different resolution, this list of dimensions will be used to specify the limits along the x- and y-axis of the array for each sample.
split.labels	Only works if the features are specified by character vectors. The plot will be split into one plot for each group label, highlighting the labelled spots.
pxum	A data.frame object with columns for 'x', 'xend', 'y' and 'sample' used for facetted plots.
sb.size	Defines the size of the scalebar
dark.theme	Switches color of scalebar to 'white'
limits	Sets the range of the colorbar values
label.by	Feature to relabel facets by. By default, facets are given a unique section number ranging grom 1 to the number of sections available in the 'Staffli' object. If you want to relabel these facets you can pass the name of a column that keeps the labels that you want to use. For example, if you wish to rename the facets to use labels defined by a charcater vector in column "section_id" in your meta.data slot, you can pass 'label.by = "section_id"' to relabel the facets. Only works for categorical group variables with where the number of groups is less than or equal to the number of tissue sections in your Staffli object.
...	Parameters passed to geom_point()

jbergenstrahle/STUtility documentation built on March 14, 2023, 7:15 a.m.