monocle_wrapper {uSORT} | R Documentation |
A wrapper function for Monocle sorting method
monocle_wrapper(log2_exp, expression_data_raw, lod = 1)
log2_exp |
An log2 transformed expresssion matrix containing n-rows of cells and m-cols of genes. |
expression_data_raw |
A data frame containing raw expression values, with rownames of cells and colnames of genes. |
lod |
A value of limit of detection in the unit of TPM/CPM/RPKM. |
A data frame containing single column of ordered sample IDs.
set.seed(15) da <- iris[sample(150, 150, replace = FALSE), ] rownames(da) <- paste0('spl_',seq(1,nrow(da))) d <- da[,1:4] dl <- da[,5,drop=FALSE] #res <- monocle_wrapper(log2_exp = d, expression_data_raw = d) #dl <- dl[match(res,rownames(dl)),] #annot <- data.frame(id = seq(1,length(res)), label=dl, stringsAsFactors = FALSE) #ggplot(annot, aes(x=id, y=id, colour = label)) + geom_point() + theme_bw()