plot3-reducedDim-method: 3D plotting function
In wjawaid/bglab: Berthold Gottgens lab scRNA seq

Description Usage Arguments Details Value Author(s)

3D plotting function

## S4 method for signature 'reducedDim'
plot3(object, colorBy = "", plotCols = NULL,
  legendSize = 1, legendOffset = 0.2, legPlac = 1:3, legPos = "front",
  negLeg = FALSE, plotLegend = TRUE, legVert = 1, legTextPos = 1,
  axLabs = "Component", doPath = FALSE, doTree = FALSE,
  selectedPath = NULL, useDims = 1:3, selectedCells = c(NA, NULL),
  legendTitle = "", diamWidth = 2, diamCol = "black", returnID = FALSE,
  na.col = "Black", bringToFront = TRUE, project2D = NULL,
  opacity = NULL, size = 5, pch = 20, outline = NULL, ...)

`object`	A Reduced Dimension object
`colorBy`	Character or numeric vector. Character vectors will be converted to a factor and cells coloured accordingly. Cell color can be supplied in the plotCols parameter. If not supplied the ggplots2 coloring scheme will be adopted.
`plotCols`	Colors to use for the plot
`legendSize`	Controls the size of the legend
`legendOffset`	Distance from the edge of the axis to place the legend as a proportion of the length of the axis.
`legPlac`	Controls the axis along which the legend is placed.
`legPos`	Controls the depth at which the legend is placed. Default is "front".
`negLeg`	Moves the legend to the other extreme of the axis
`plotLegend`	Logical value. Default is "True"
`legVert`	Controls the vertical orientation of the legend
`legTextPos`	Controls the position of the legend text
`axLabs`	Prefix with which to label the axes.
`doPath`	Logical value controlling whether the diameter path is plotted
`doTree`	Logical calue controlling whether the minimum spanning tree is plotted
`selectedPath`	The path to plot. Default is NULL and will plot the diameter path.
`useDims`	The dimensions of the the dimensionality reduced objects to use
`selectedCells`	The selected cells to plot
`legendTitle`	Legend title.
`diamWidth`	Width of diameter path to be plotted
`diamCol`	Color of diameter path
`returnID`	Whether to return the rgl plot id. For use with selecting cells.
`na.col`	Colour for missing values. Default is Black.
`bringToFront`	To bring higher colours to fore.
`project2D`	Default NULL. Projects 3D graph into 2D by the given transformation matrix. This matrix must have been produced using `getMVP` on an open rgl device.
`opacity`	NULL. If given will use the data given in this column to set point opacity. Ensure these are numeric and between 0-1
`size`	Default 5. Sets point size.
`pch`	Default 20. Sets point size.
`outline`	Default is NULL. If require an outline set this to required colour.
`...`	Parameters to be passed to `plot3d` function.