plotOrderedExpression {scHOT} | R Documentation

## 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
    )

### 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

[Package scHOT version 1.6.0 Index]