plot_trajectory: Visualize pseudotimes on locations.

In shangll123/SpatialPCA: Spatially Aware Dimension Reduction for Spatial Transcriptomics

Visualize pseudotimes on locations.

Description

This function visualizes pseudotimes on locations.

Usage

plot_trajectory(
  pseudotime,
  location,
  clusterlabels,
  gridnum,
  color_in,
  pointsize = 5,
  arrowlength = 0.2,
  arrowsize = 1,
  textsize = 22
)

Arguments

pseudotime	A length n vector of pseudotime inferred from Slingshot.
location	A n by 2 data frame of spot locations.
clusterlabels	A vector of integers, the cluster labels for each spot
gridnum	Number of grids that evenly segment the whole tissue section.
color_in	A vector of character strings representing colors for each cluster.
pointsize	An integer, the point size of each spot
arrowlength	An integer, the length of arrows inside a grid between one spot with smallest pseudotime and largest pseudotime.
arrowsize	An integer, the size of arrows inside a grid between one spot with smallest pseudotime and largest pseudotime.
textsize	An integer, the size of text in the figure.

Value

A ggplot object.

Pseudotime	A ggplot object visualizing pseudotime on locations.
Arrowplot1	A ggplot object for arrows pointing from smallest pseudotime and largest pseudotime in each grid.
Arrowplot2	A ggplot object for arrows pointing from largest pseudotime and smallest pseudotime in each grid.
Arrowoverlay1	A ggplot object for arrows pointing from smallest pseudotime and largest pseudotime in each grid, overlayed on clustering plot.
Arrowoverlay2	A ggplot object for arrows pointing from largest pseudotime and smallest pseudotime in each grid, overlayed on clustering plot.

shangll123/SpatialPCA documentation built on April 17, 2024, 3:15 a.m.