plotHigherOrderSequence {scHOT} | R Documentation |
the plotHigherOrderSequence function plots weighted higher order statistic vectors (stored in higherOrderSequence) as line plots
plotHigherOrderSequence( scHOT, gene, positionType = NULL, branches = NULL, positionColData = NULL )
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) |
ggplot
object with line plots
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"))