Plot_DiffusionMap: Visualize diffusion map

In ChenWeiyan/LandSCENT: Landscape Single Cell Entropy

Description

This function visualizes the diffusion map in 2D or 3D plots

Usage

Plot_DiffusionMap(
  Integration.l,
  dim = c(1, 2, 3),
  color_by = c("SR", "DPT"),
  TIPs = c(1, 2, 3),
  phi = 20,
  theta = 40,
  bty = "g",
  ...,
  PDF = FALSE
)

Arguments

Integration.l	Typically, it is the output from DoDiffusionMap function
dim	A numeric vector. Diffusin components order in the plot axes. And the sign of evrey entry indicates the direction of component. Default is c(1, 2, 3)
color_by	Indicating the variable used for coloring. SR means the plot is colored by SR values. DPT means the plot is colored by diffusion pseudotime
TIPs	Specifying which trajectory paths should be shown on the diffusion maps. Only available in 2D plot and when color_by was set to be DPT
phi	The angles defining the viewing direction. phi gives the colatitude. Default is 20
theta	The angles defining the viewing direction. theta gives the azimuthal direction. Default is 40
bty	The type of the box, the default g draws grey background with white grid lines. Note: the bty = "f", "b", "b2", "bl" can also be specified for this argument
...	Additional arguments passed to the 3D plotting methods
PDF	A logical. Output figure via pdf file or not, default is FALSE

Value

A pdf file contains the generated figure or a ggplot object

References

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.

Teschendorff, Andrew E., Peter Sollich, and Reimer Kuehn. Signalling entropy: A novel network-theoretical framework for systems analysis and interpretation of functional omic data. Methods 67.3 (2014): 282-293. doi: 10.1016/j.ymeth.2014.03.013.

Examples

## Not run: 
data(Example.m)
data(net13Jun12.m)
Integration.l <- DoIntegPPI(exp.m = Example.m[, c(1:58,61:84,86:98,100)], ppiA.m = net13Jun12.m)
data(SR.v)
Integration.l$SR <- SR.v
InferPotency.o <- InferPotency(Integration.l)
DoDM.o <- DoDiffusionMap(InferPotency.o)
Plot_DiffusionMap(DoDM.o)

## End(Not run)

ChenWeiyan/LandSCENT documentation built on Aug. 28, 2020, 9:55 p.m.