plotOrderedExpression

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

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