#' Dimension reduction for high dimensional data
#'
#' Apply dimension reduction on the cytof expression data,
#' with method \code{pca}, \code{tsne} or \code{isomap}.
#'
#' @param data Input expression data matrix.
#' @param method Method chosed for dimensition reduction, must be one of \code{isomap}, \code{pca} or \code{tsne}.
#' @param out_dim The dimensionality of the output.
#' @param isomap_distMethod Method for distance calcualtion for \code{isomap}.
#' @param isomap_k Number of shortest dissimilarities retained for a point, parameter for \code{isomap} method.
#' @param isomap_ndim Number of axes in metric scaling, parameter for \code{isomap} method.
#' @param isomapFragmentOK What to do if dissimilarity matrix is fragmented, parameter for \code{isomap} method.
#' @param ... Other parameters passed to Rtsne
#' @return a matrix of the dimension reducted data, with colnames method_ID, and rownames same as the input data.
#'
#' @importFrom vegan vegdist spantree isomap
#' @importFrom Rtsne Rtsne
#' @import stats
#' @export
#' @examples
#' data(iris)
#' in_data <- iris[, 1:4]
#' out_data <- cytof_dimReduction(in_data, method = "tsne")
cytof_dimReduction <- function(data,
method = c("tsne", "pca", "isomap", "NULL"),
out_dim = 2,
isomap_distMethod = "euclidean",
isomap_k = 5,
isomap_ndim = NULL,
isomapFragmentOK = TRUE,
...) {
data <- as.matrix(data)
rnames <- row.names(data)
method <- match.arg(method)
if(method == "NULL"){
return(NULL)
}
switch(method,
tsne={
cat(" Runing t-SNE...")
tsne_out <- Rtsne(data, initial_dims = ncol(data),
dims = 2,
check_duplicates = FALSE,
pca = TRUE, ...)
mapped <- tsne_out$Y
},
pca={
cat(" Runing PCA...")
mapped <- prcomp(data, scale = TRUE)$x
},
isomap={
cat(" Runing ISOMAP...")
if (is.null(isomap_ndim))
isomap_ndim <- ncol(data)
ord <- tryCatch({
dis <- vegdist(data, method = isomap_distMethod)
isomap(dis, ndim = isomap_ndim, k = isomap_k, fragmentedOK = isomapFragmentOK)
}, error=function(cond) {
message("Runing isomap failed")
message("Here's the original error message:")
message(cond)
return(NULL)
})
if(is.null(ord)){
mapped <- NULL
}else{
if(nrow(ord$points) != nrow(data)){
message("Run ISOMAP failed!")
return(NULL)
}
mapped <- ord$points
}
})
## organize output
if(ncol(mapped) < out_dim){
out_dim <- ncol(mapped)
message("Run ",method," for dimensional reduction, out dimension coerced to ",out_dim)
}
mapped <- mapped[ ,c(1:out_dim)]
colnames(mapped) <- paste(method, c(1:out_dim), sep = "_")
rownames(mapped) <- rnames
cat("DONE\n")
return(mapped)
}
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