plotHigherOrderSequence {scHOT} | R Documentation

## plotHigherOrderSequence

### Description

the plotHigherOrderSequence function plots weighted higher order statistic vectors (stored in higherOrderSequence) as line plots

### Usage

    plotHigherOrderSequence(
      scHOT,
      gene,
      positionType = NULL,
      branches = NULL,
      positionColData = NULL
    )

### Arguments

`scHOT` | A scHOT object with higherOrderSequence in scHOT_output slot
`gene` | is either a logical vector matching rows of entries in wcorsList, or a character of a gene
`positionType` | A string indicates the position type, either trajectory or spatial
`branches` | A character indicates that the colnames stored the branch information in colData (for trajectory type of data)
`positionColData` | A vector indicates column names of colData that stored the postion informaton (for spatial type of data)

### Value

`ggplot` object with line plots

### Examples

    data(liver)

    scHOT_traj <- scHOT_buildFromMatrix(
    mat = liver$liver_branch_hep,
    cellData = list(pseudotime = liver$liver_pseudotime_hep),
    positionType = "trajectory",
    positionColData = "pseudotime")
    scHOT_traj
    plotColouredExpression(scHOT_traj, c("Cdt1","Top2a"), n = 5)

    scHOT_traj <- scHOT_addTestingScaffold(scHOT_traj,
    t(as.matrix(c("Cdt1", "Top2a"))))
    scHOT_traj <- scHOT_setWeightMatrix(scHOT_traj,
    positionColData = c("pseudotime"),
    positionType = "trajectory",
    nrow.out = NULL,
    span = 0.25)
    scHOT_traj <- scHOT_calculateGlobalHigherOrderFunction(scHOT_traj,
                                                          higherOrderFunction =
                                                          weightedSpearman,
                                                         higherOrderFunctionType =
                                                         "weighted")

    scHOT_traj <- scHOT_calculateHigherOrderTestStatistics(scHOT_traj,
                                                          higherOrderSummaryFunction =
                                                          sd)

    slot(scHOT_traj, "scHOT_output")
    plotHigherOrderSequence(scHOT_traj, c("Cdt1_Top2a"))

[Package scHOT version 1.0.0 Index]