HSVPlot3D: Plots the values of a feature in 3D

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

Plots the values of a feature in 3D

Description

Plots the values of a feature in 3D

Usage

HSVPlot3D(
  object,
  features,
  mode = c("cloud", "spots"),
  zcoords = NULL,
  spots = NULL,
  min.cutoff = NA,
  max.cutoff = NA,
  slot = "data",
  blend = FALSE,
  pt.size = NULL,
  pt.alpha = 1,
  cols = NULL,
  add.alpha = FALSE,
  add.margins = 0,
  channels.use = NULL,
  scene = "scene1",
  return.data = FALSE,
  dark.theme = TRUE,
  rescale = TRUE,
  verbose = FALSE
)

Arguments

object	Seurat object
features	An Assay feature (e.g. a gene name - "MS4A1") A column name from meta.data (e.g. mitochondrial percentage - "percent.mito") A column name from dimensionality reduction output (e.g. principal component 1 - "PC_1")
mode	Select mode to display the 3D stack in. The default 'cloud' option will use the stacked point patterns as a scaffold for the 3D visualization whereas the 'spots' options will use the spot coordinates instead.
zcoords	Vector of z coordinates with the same length as the number of sections in the dataset [default: 1:#sections]
spots	Vector of spots to plot (default is all spots)
min.cutoff, max.cutoff	Vector of minimum and maximum cutoff values for each feature, may specify quantile in the form of 'q##' where '##' is the quantile (eg, 'q1', 'q10'). This can be useful if you have outlier values that skew the colorscale in the plot. For example, if you specify 'q1', you will trim of values below the 1st percentile. [default: no cuttoffs]
slot	Which slot to pull the data from? [default: 'data']
blend	Scale and blend expression values to visualize coexpression of two features (this options will override other coloring parameters). See 'Blending values' below for a more thourough description.
pt.size	Sets the size of points in the 3D plot
pt.alpha	Sets the opacity of the points
cols	Character vector of colors with equal length to the number of features. These colors will override the selection of HSV colors and can therefore not be encoded in the same way. Instead of tuning the saturation/value parameters we can add an alpha channel, making spots with values close to zero completely transparent. This has to be activated by setting 'add.alpha = TRUE'
add.alpha	Adds opacity to colors.
add.margins	Add margins along z axis to push sections closer to each other
channels.use	Color channels to use for blending. Has to be a character vector of length 2 or 3 with "red", "green" and "blue" color names specified [default: c("red", "green", "blue)]
scene	Give the scene a name to allow for multiple subplots
return.data	return the data.frame with x,y coordinates and interpolated values instead of plotting
dark.theme	Draws the plot with a dark theme
rescale	Rescale each feature column separately from 0 to 1 range. If set to FALSE, all feature columns will be scaled together from 0 to 1 and preserve the relative differencies
verbose	Print messages

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