R/CommPath-object.R

In yingyonghui/CommPath:

#setClassUnion(name='exprMatrix', members=c("matrix", "dgCMatrix"))

#' To define the CommPath object and the key slots
#' @slot data normalized expression matrix
#' @slot cell.info vector of cell labels
#' @slot meta.info list of important parameters used during the analysis
#' @slot LR.marker data frame of the differential expression test result of ligands and receptors
#' @slot interact list containing information of LR interaction among clusters
#' @slot interact.filter list containing information of filtered LR interaction among clusters
#' @slot pathway list containing information of pathways associated with ligands and receptors
#' @slot pathway.net list containing the integrated information of the statistics of LR interactions and associated pathways
#' @importFrom methods setClass
#' @exportClass CommPath
CommPath <- setClass("CommPath",
	slots = c(data = 'ANY',
	cell.info = 'data.frame',
	meta.info = 'list',
	LR.marker = 'data.frame',
	interact = 'list',
	interact.filter = 'list',
	pathway = 'list',
	pathway.net = 'list'
	)
)

#' To create a CommPath object
#' @param expr.mat Matrix or data frame of expression matrix, with genes in rows and cells in columns
#' @param cell.info Vector of lables indicating identity classes of cells in the expression matrix, and the order of lables should match the order of cells in the expression matrix; or a data frame containing the meta infomation of cells with the row names matching the cells in the expression matrix and a column named as "Cluster" must be included to indicate identity classes of cells
#' @param species Species, either 'hsapiens'('human'), 'mmusculus'('mouse'), or 'rnorvegicus'('rat')
#' @return CommPath object
#' @export
createCommPath <- function(expr.mat, cell.info, species){
	if (length(species) > 1){
		stop("Select one species from hsapiens (human), mmusculus (mouse), rnorvegicus (rat), drerio (zebrafish), dmelanogaster (fruitfly), or celegans (worm)")
	}else if(species=='human'){
		species <- 'hsapiens'
	}else if(species=='mouse'){
		species <- 'mmusculus'
	}else if(species=='rat'){
		species <- 'rnorvegicus'
	}else if(species=='zebrafish'){
		species <- 'drerio'
	}else if(species=='fruitfly'){
		species <- 'dmelanogaster'
	}else if(species=='worm'){
		species <- 'celegans'
	}


	if (!(species %in% c('hsapiens', 'mmusculus', 'rnorvegicus', 'drerio', 'dmelanogaster', 'celegans'))){
		stop("Select one species from hsapiens (human), mmusculus (mouse), rnorvegicus (rat),drerio (zebrafish), dmelanogaster (fruitfly), or celegans (worm)")
	}

	if(is.vector(cell.info) | is.factor(cell.info)){
		if(length(cell.info)!=ncol(expr.mat)){
			stop('The input cell.info is vector, and the length of cell.info should match the ncol of expr.mat!')
		}
		cell.info <- data.frame(Cluster=cell.info)
		rownames(cell.info) <- colnames(expr.mat)
	}else if(is.data.frame(cell.info)){
		if(nrow(cell.info)!=ncol(expr.mat)){
			stop('The input cell.info is a data frame, and the row names of cell.info should match the column names of expr.mat!')
		}
		if(any(rownames(cell.info) !=  colnames(expr.mat))){
			stop('The input cell.info is a data frame, and the row names of cell.info should match the column names of expr.mat!')
		}
	}else{
		stop('Either input a vector or a data frame for cell.info')
	}
	object <- methods::new(Class="CommPath",
		data = as(expr.mat, "dgCMatrix"),
		cell.info = cell.info,
		meta.info = list(species=species, logFC.thre=NULL, p.thre=NULL),
		LR.marker = data.frame(),
		interact = list(),
		interact.filter = list(),
		pathway = list(),
		pathway.net = data.frame()
	)

	return(object)
}


#' Show method for CommPath
#' @param object A CommPath object
#' @docType methods
setMethod(f="show", signature="CommPath", definition=function(object) {
	cat("An object of class", class(object), "with\n",
		nrow(x = object@data), "genes *", ncol(x = object@data), "cells.\n"
	)
	invisible(x = NULL)
})