branchpointPreferenceLayout: Generate Branchpoint Preference Layout

In farrellja/URD: URD

Description

This generates a preference layout for a single branchpoint. In it, cells are laid out along the y-axis according to pseudotime, and along the x-axis according to preference, which is related to the ratio of their visits from the two segments under consideration. (Preference is the difference in the visit frequency by random walks from the two segments, divided by the sum of the visits from both segments.) This preference layout is used as input to plotBranchpoint.

Usage

branchpointPreferenceLayout(
  object,
  pseudotime,
  lineages.1,
  lineages.2,
  parent.of.lineages,
  opposite.parent,
  min.visit = 0
)

Arguments

object	An URD object
pseudotime	(Character) Pseudotime to use (i.e. a column name of @pseudotime)
lineages.1	(Character) Segment(s) for the left side of the branchpoint
lineages.2	(Character) Segment(s) for the right side of the branchpoint
parent.of.lineages	(Character) Segment that is upstream of the branchpoint
opposite.parent	(Character vector) Siblings of the parent.of.lineages.
min.visit	(Numeric) Minimum visitation frequency to appear in the layout

Value

A branchpoint layout that can be used as input to plotBranchpoint

Examples

# Visualize tree with segments labeled
plotTree(object, label.segments=T)
# Notochord is segment 32, prechordal plate is segment 29, their 
# parent axial mesoderm is segment 79, and the axial mesoderm's 
# siblings are segments 72 and 78.

# Generate axial mesoderm branchpoint layout
np.layout <- branchpointPreferenceLayout(object, pseudotime = "pseudotime", 
lineages.1 = "29", lineages.2 = "32", parent.of.lineages = "79", 
opposite.parent = c("72","78"), min.visit = 1)

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