Description Usage Arguments Value Examples
View source: R/branchpointPlot.R
This plots gene expression or metadata on a branchpoint preference plot generated
by branchpointPreferenceLayout
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | 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
)
|
object |
An URD object |
branchpoint.layout |
The output of |
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 |
color.scale |
(Character vector) Vector of colors to use as a color scale if |
discrete.colors |
(Character vector) Vector of colors to use as a color scale if |
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. |
A ggplot2 object
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | # 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)
|
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