Plot_LandSR: Plot Landscape with potency states
In ChenWeiyan/LandSCENT: Landscape Single Cell Entropy

Description Usage Arguments Details Value References Examples

Density based visualization tool to generate figures that give the cell density distribution against potency states

Plot_LandSR(
  Integration.l,
  coordinates = NULL,
  num_grid = 50,
  phi = 20,
  theta = 20,
  colpersp = NULL,
  colimage = NULL,
  colkeypersp = list(length = 0.2, width = 0.4, shift = 0.15, cex.axis = 0.6, cex.clab
    = 0.65),
  colkeyimage = list(length = 0.2, width = 0.4, shift = -0.15, cex.axis = 0.6, cex.clab
    = 0.65),
  lighting = FALSE,
  lphi = 90,
  bty = "b",
  scale_z = TRUE,
  PDF = TRUE
)

`Integration.l`	Typically, it is the output from `InferLandmark` function
`coordinates`	Optional. The previous reduced dimension coordinates, with rows lalabeling cells and two colums labeling reduced dimensions
`num_grid`	Number of grid points in each direction. Can be scalar or a length-2 integer vector
`phi`	The angles defining the viewing direction. phi gives the colatitude
`theta`	The angles defining the viewing direction. theta gives the azimuthal direction
`colpersp`	Color palette to be used for the colvar variable, i.e. specific potency state cell density. If colpersp is NULL (default) and colvar is specified, then a red-yellow-blue colorscheme will be used.
`colimage`	Color palette to be used for the colvar variable, i.e. the cell density. If colimage is NULL (default) and colvar is specified, then a red-magenta-white colorscheme will be used.
`colkeypersp`	A logical, or a list (default) with parameters for the color key (legend). List parameters should be one of side, plot, length, width, dist, shift, addlines, col.clab, cex.clab, side.clab, line.clab, adj.clab, font.clab and the axis parameters at, labels, tick, line, pos, outer, font, lty, lwd, lwd.ticks, col.box, col.axis, col.ticks, hadj, padj, cex.axis, mgp, tck, tcl, las. The defaults for the parameters are length = 0.2, width = 0.4, shift = 0.15, cex.axis = 0.6, cex.clab = 0.65 The default is to draw the color key on side = 4, i.e. in the right margin. If colkeypersp = NULL then a color key will be added only if col is a vector. Setting colkeypersp = list(plot = FALSE) will create room for the color key without drawing it. if colkeypersp = FALSE, no color key legend will be added. See more details in ?plot3D::persp3D
`colkeyimage`	A logical, or a list (default) with parameters for the color key (legend). List parameters should be one of side, plot, length, width, dist, shift, addlines, col.clab, cex.clab, side.clab, line.clab, adj.clab, font.clab and the axis parameters at, labels, tick, line, pos, outer, font, lty, lwd, lwd.ticks, col.box, col.axis, col.ticks, hadj, padj, cex.axis, mgp, tck, tcl, las. The defaults for the parameters are length = 0.2, width = 0.4, shift = -0.15, cex.axis = 0.6, cex.clab = 0.65 The default is to draw the color key on side = 4, i.e. in the right margin. If colkeyimage = NULL then a color key will be added only if col is a vector. Setting colkeyimage = list(plot = FALSE) will create room for the color key without drawing it. if colkeyimage = FALSE, no color key legend will be added. See more details in ?plot3D::image3D
`lighting`	A logical. If TRUE, the facets will be illuminated, and colors may appear more bright. Default is FALSE
`lphi`	if finite values are specified for lphi, the surface is shaded as though it was being illuminated from the direction specified by colatitude lphi
`bty`	The type of the box ("b" or "f"), the default ("b") only drawing background panels
`scale_z`	A logical, whether to scale the density z value or not
`PDF`	A logical. Output figure via pdf file or not, default is TRUE

Density based visualization tool to generate figures that give the cell density distribution against potency states

A pdf file contains the generated figures

Integration.l If coordinates provided, it will be a list object integrates the input list and coordinates

Teschendorff AE, Tariq Enver. Single-cell entropy for accurate estimation of differentiation potency from a cell’s transcriptome. Nature communications 8 (2017): 15599. doi: 10.1038/ncomms15599.

data(tsne.o)
data(potS.v)
data(SR4.v)
potS.v <- 4 - potS.v
InferLandmark.o <- list(potencyState = potS.v, SR = SR4.v, coordinates = tsne.o)

LandSR.o <- Plot_LandSR(InferLandmark.o, PDF = FALSE)