plotSpatialOverlay: overlay plots

In Nanostring-Biostats/SpatialOmicsOverlay: Spatial Overlay for Omic Data from Nanostring GeoMx Data

overlay plots

Description

overlay plots

Usage

plotSpatialOverlay(
  overlay,
  colorBy = "sampleID",
  hiRes = TRUE,
  alpha = 1,
  legend = TRUE,
  scaleBar = TRUE,
  image = TRUE,
  fluorLegend = FALSE,
  ...,
  corner = "bottomright",
  scaleBarWidth = 0.2,
  scaleBarMicrons = NULL,
  scaleBarColor = NULL,
  scaleBarFontSize = 6,
  scaleBarLineSize = 1.5,
  textDistance = 2
)

Arguments

overlay	SpatialOverlay object
colorBy	annotation to color by
hiRes	generated figures are either high resolution or print quickly. Note: hiRes and outline ggplots use fill, lowRes uses color
alpha	opacity of overlays
legend	should legend be plotted
scaleBar	should scale bar be plotted
image	should image be plotted, image must be added to SpatialOverlay object
fluorLegend	should viz marker on the image be added to legend
...	additional parameters for scale bar line & text, will affect both
corner	where in the figure should the scale bar be printed. Options: "bottomright" "topright" "bottomleft" "topleft" "bottomcenter" "topcenter"
scaleBarWidth	percent of total figure the scale bar should take up
scaleBarMicrons	specific microns to set scale bar at, overrides scaleBarWidth if set
scaleBarColor	scale bar & text color
scaleBarFontSize	font size
scaleBarLineSize	width of line
textDistance	text's distance from scale bar.

Value

gp

Note

hiRes and outline ggplots use fill, lowRes uses color

Examples

muBrain <- readRDS(unzip(system.file("extdata", "muBrainSubset_SpatialOverlay.zip",
                                    package = "SpatialOmicsOverlay")))
                             
plotSpatialOverlay(overlay = muBrain, legend = FALSE,  
                   hiRes = FALSE, scaleBar = FALSE)

Nanostring-Biostats/SpatialOmicsOverlay documentation built on April 20, 2024, 5:36 a.m.