genePattern

State transition pattern of each gene with flexible switch point definitions

Usage

genePattern(
  data,
  switch_method = c("zero_crossing", "threshold_crossing", "max_first_derivative"),
  cutoff = 0
)

Arguments

data

a single cell expression matrix or data.frame with rows as genes and columns as cells. Cells should follow the order of pseudo time.

switch_method

character specifying switch point definition. Default is "zero_crossing".

cutoff

numeric baseline used only when switch_method = "threshold_crossing".

Value

A dataframe of state transition pattern

Details

#' @title PreprocessPseudotime #' @description Pseudotimecascade Preprocess #' @details This function generates a table that performs Pseudotimecascade #' @param data a single cell expression matrix or data.frame with rows as genes and columns as cells. Cells should follow the order of pseudo time #' @param gl marked gene list #' @return A Heatmap-class object #' @export PreprocessPseudotime PreprocessPseudotime <- function(data, gl) gene_group <- genePattern(data) plotdata <- data[rownames(gene_group), ] p <- PseudotimeHeatmap(plotdata, gl, as.matrix(gene_group)[, "pattern"]) return(p)

This function generates the state transition pattern of input gene along pseudotime. Switch points can be defined by:

• "zero_crossing": sign change around 0 (default).

• "threshold_crossing": sign change around a user-defined cutoff.

• "max_first_derivative": position with the largest absolute first derivative.

Author

Zhicheng Ji, Changxin Wan, Beijie Ji