Generates a 3D spatial feature plot from a SpaMTP object

This function generates an interactive plotly 3D spatial plot of 2 specified features. These features can include a combination of metabolites and/or genes expression values, or numerical meta.data values. Features must be numeric values. Please see SpaMTP Additional Features vignette for instructions on how to plot catagorical data, or > 2 features.

Usage

Plot3DFeature(
  data,
  features,
  assays = c("SPT", "SPM"),
  slots = "counts",
  between.layer.height = 100,
  names = NULL,
  size = 3,
  col.palette = "Reds",
  x.axis.label = "x",
  y.axis.label = "y",
  z.axis.label = "z",
  show.x.ticks = FALSE,
  show.y.ticks = FALSE,
  show.z.ticks = FALSE,
  show.image = NULL,
  plot.height = 800,
  plot.width = 1500,
  image.sf = "lowres",
  downscale.image = NULL
)

Arguments

data: A SpaMTP Seurat Object.
features: A character vector specifying the features to be plotted.
assays: A character vector specifying the Seurat Object assays to be used for plotting (default = c("SPT", "SPM")).
slots: A character vector specifying the assay slots to be used for plotting (deafult = "counts").
between.layer.height: A numeric value specifying the height between layers (default = 100).
names: A character vector specifying custom names for the features. If NULL will use feature names (default = NULL).
size: A numeric value specifying the size of markers in the plot (default = 3).
col.palette: Character list defining the colour palettes to use for plotting. If only 1 is supplied than it will be used for both variables. Possible palettes to use are: Blackbody,Bluered,Blues,Cividis,Earth,Electric,Greens,Greys,Hot,Jet,Picnic,Portland,Rainbow,RdBu,Reds,Viridis,YlGnBu,YlOrRd (default = "Reds").
x.axis.label: A character string specifying the label for the x-axis (default = "x").
y.axis.label: A character string specifying the label for the y-axis (default = "y").
z.axis.label: A character string specifying the label for the z-axis (default = "z").
show.x.ticks: A logical value specifying whether to show ticks on the x-axis (default = FALSE).
show.y.ticks: A logical value specifying whether to show ticks on the y-axis (default = FALSE).
show.z.ticks: A logical value specifying whether to show ticks on the z-axis (default = FALSE).
show.image: Character string specifying the image name to plot. If NULL then no image is plot (default = NULL).
plot.height: Numeric value defining the height of the returned plot (default = 800).
plot.width: Numeric value defining the width of the returned plot (default = 1500).
image.sf: Character string defining the image scalefactor to use (default = "lowres").
downscale.image: Numeric value defining the amount to downscale the image by. This parameter is only necessary when show.image != NULL. Downscaling the image is not necessary, however when rendering plotly to HTML excessively large images can cause issues whereby setting a downscaling value can improve this (default = NULL).

Value

A 3D Plotly plot

Examples

# Plot3DFeature(data = my_data, features = c("gene1", "gene2"), assays = c("SPT", "SPM"), show.image = "slice1")