DimPlot3D: Plots a selected dimensionality reduction vector in 3D

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

Plots a selected dimensionality reduction vector in 3D

Description

This function is similar to the ST.DimPlot but works for 3D stacked data. First, you need to mask and align the tissue sections in your Seurat object and run the Create3DStack function to create the 3D stack from the aligned images.

Usage

DimPlot3D(
  object,
  spots = NULL,
  dims = 1,
  reduction = NULL,
  mode = c("cloud", "spots"),
  pts.downsample = 5e+05,
  zcoords = NULL,
  min.cutoff = NA,
  max.cutoff = NA,
  blend = FALSE,
  pt.size = NULL,
  pt.alpha = 1,
  cols = c("navyblue", "cyan", "yellow", "red", "dark red"),
  add.alpha = FALSE,
  add.margins = 0,
  channels.use = NULL,
  scene = "scene1",
  return.data = FALSE,
  dark.theme = FALSE,
  verbose = FALSE
)

Arguments

object	Seurat object
spots	Subset spots to plot
dims	Dimensions to plot [default: 1]. Only one dimension can be plotted at the time unless the blend option is activated, in which case you can plot 2 or three dimensions at the time.
reduction	Reduction object to pull data from [e.g. 'umap', 'pca', 'ica', 'NMF', ...]
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.
pts.downsample	Downsample the point cloud to this number [default: 5e5].
zcoords	Vector of z coordinates with the same length as the number of sections in the dataset [default: 1:number_of_sections]
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]
blend	Scale and blend expression values to visualize coexpression of two dims (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. Only active if 'add.alpha = FALSE'
cols	Colors used to create a colorscale
add.alpha	Adds opacity to points scaled by feature values. See opacity section for more details.
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
verbose	Print messages

Blending values

The blend option can be useful if you wish to visualize multiple dimensionality reduction simultaneuosly and works for two or three value vectors. Each of the selected vectors are rescaled from 0 to 1 and are used as RGB color channels to produce mixed color for each spot. This can be particularly useful when looking at overlapping value vectors. For example, if you are looking at two overlapping value vectors "A" and "B" and use the blend option, the "A" values will be encoded in the "red" channel and the "B" values in the "green" channel. If a spot is purely "A" the color will be red and if it is purely "B" it will green. Any mixture of "A" and "B" will produce a color between red and green where a 50/50 mixture gives yellow color.

distance between tissue sections

The distance between adjacent tissue sections is by default set to 1 with the z axis ranging from 0 to the number of sections. You can control the distances manually by converting the z coordinates using the 'zcoords'. The range of the z axis can be controlled to either force the sections closer to each other or adding distance between them. This can be done using the 'add.margins' option which accepts a numeric value that will stretch out the z axis range. For example, if you have 6 sections and 'add.margins = 20', the z axis will range from [-20, 26] and therefore push the sections closer to each other.

opacity

Sometimes it can be useful to add some opacity to the points to make it easier to look at 3D structures. If 'pt.alpha' is specified, the same opacity will be applied to all points. If 'add.alpha' is active, the opacity will be scaled with the feature values, meaning that the points with the lowest feature values will be transparent. 'add.alpha' does not work for blended values.

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