plotOrderedExpression: plotOrderedExpression

In shazanfar/scHOT: single-cell higher order testing

plotOrderedExpression

Description

the plotOrderedExpression function plots expression vectors along branches and genes as ribbon plots

Usage

plotOrderedExpression(
  scHOT,
  genes,
  positionType = NULL,
  branches = NULL,
  ranked_by = NULL,
  xvals = NULL,
  subsetBranch = NULL,
  facet = FALSE,
  positionColData = NULL,
  assayName = NULL,
  point_size = 3
)

Arguments

scHOT	A scHOT object, where the expression data is stored in the assay slot, with assay name "expression".
genes	is a character vector for gene names
positionType	A string indicates the position type, either trajectory or spatial
branches	A character indicates that the colnames stored the branch information in colData
ranked_by	A character indicates that the colnames stored the ranking information of the cells in colData, such as trajectory time
xvals	A character indicates that the colnames stored in colData of the x-values associated with the samples in branchData
subsetBranch	subsetBranch is a character vector containing the names of the branches to be plotted. If NULL it will plot all branches
facet	can either be FALSE, "branch", "gene", or "both"
positionColData	A vector indicates column names of colData that stored the postion informaton (for spatial type of data)
assayName	the name of the assay that are used to plot.

Value

ggplot a ggplot object for ribbon plot with points

shazanfar/scHOT documentation built on June 29, 2023, 5:29 p.m.