plotBranchpoint: Plot Data On Branchpoint Layout

In farrellja/URD: URD

Description

This plots gene expression or metadata on a branchpoint preference plot generated by branchpointPreferenceLayout.

Usage

plotBranchpoint(
  object,
  branchpoint.layout,
  label,
  label.2 = NULL,
  label.type = "search",
  populations = NULL,
  visited.size = T,
  point.alpha = 0.2,
  pt.lim = NULL,
  color.scale = NULL,
  discrete.colors = NULL,
  ylab = "Pseudotime",
  xlab = "Preference",
  title = label,
  axis.lines = T,
  legend = T,
  fade.low = 0.5
)

Arguments

object	An URD object
branchpoint.layout	The output of branchpointPreferenceLayout
label	(Character) Value to plot
label.2	(Character) If dual-color plotting, the second value to plot.
label.type	(Character)
populations	(Character vector, length 2) Labels for the two populations on the x-axis.
visited.size	(Logical) Should the size of points reflect how frequently they were visited by the random walks (to emphasize the more confident data points)
point.alpha	(Numeric) Transparency of points
pt.lim	(Numeric vector) Pseudotime (y) axis limits. Default NULL lets ggplot determine them automatically.
color.scale	(Character vector) Vector of colors to use as a color scale if label is continuous values. Does not apply if a second label is given, in which case the color scale will be red-green.
discrete.colors	(Character vector) Vector of colors to use as a color scale if label is discrete values.
ylab	(Character) Y-axis label
xlab	(Character) X-axis label
title	(Character) Plot title
axis.lines	(Logical) Plot axis lines on the plot?
legend	(Logical) Plot an expression legend?
fade.low	(Numeric) The transparency of the lowest expression points are decreased by this factor in order to prevent them from blocking the visualization of expressing cells if they are intermixed.

Value

A ggplot2 object

Examples

# Plot with a discrete label -- STAGE
plotBranchpoint(object, np.layout, label="stage.nice", 
point.alpha=0.5, populations = c("P", "N"), pt.lim=c(0.7,0.1), 
xlab="", ylab="", legend=T, axis.lines = F, fade.low=0, 
discrete.colors = stage.colors[c(1,3:12)], title="Stage")

# Define genes to plot
axial.genes.plot <- c("NANOG", "TA", "NOTO", "NTD5", 
"SHHA", "COL8A1A", "MEX3B", "GSC", "FRZB", "PRDM1A", 
"ICN", "HE1A")

# Plot expression of many genes on the branchpoint 
# npreference plot in a grid
axial.branchpoint.plots <- lapply(axial.genes.plot, function(gene) 
plotBranchpoint(object, np.layout, label=gene, point.alpha=1, 
populations = c("P", "N"), pt.lim=c(0.7,0.11), color.scale = pref.colors, 
xlab="", ylab="", title=gene, legend=F, axis.lines = F, fade.low=0.66))
gridExtra::grid.arrange(grobs=axial.branchpoint.plots, ncol=6)

farrellja/URD documentation built on June 17, 2020, 4:48 a.m.