## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE) ## ---- eval=FALSE-------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("ctgGEM") ## ----loadCTG, message=FALSE, warning=FALSE, results='hide'-------------------- library(ctgGEM) ## ----loadRaw, message=FALSE, warning=FALSE, results='hide'-------------------- # load HSMMSingleCell package library(HSMMSingleCell) # load the data data(HSMM_expr_matrix) data(HSMM_sample_sheet) data(HSMM_gene_annotation) ## ----constructctgGEMset------------------------------------------------------- toyGEMset <- ctgGEMset(exprsData = HSMM_expr_matrix, phenoData = HSMM_sample_sheet, featureData = HSMM_gene_annotation) ## ----monocleInfo-------------------------------------------------------------- monocleInfo(toyGEMset, "gene_id") <- "gene_short_name" monocleInfo(toyGEMset, "ex_type") <- "FPKM" ## ----monocleInfo2------------------------------------------------------------- # Set two marker genes to use semi-supervised mode # Alternatively, omit the next two lines to run in unsupervised mode monocleInfo(toyGEMset, "cell_id_1") <- "MYF5" # marks myoblasts monocleInfo(toyGEMset, "cell_id_2") <- "ANPEP" # marks fibroblasts ## ----TSCANinfo---------------------------------------------------------------- TSCANinfo(toyGEMset) <- "ENSG00000000003.10" ## ----sincelldistonly, eval=FALSE---------------------------------------------- # sincellInfo(toyGEMset, "method") <- "pearson" ## ----sincelldimred------------------------------------------------------------ sincellInfo(toyGEMset, "method") <- "classical-MDS" sincellInfo(toyGEMset, "MDS.distance") <- "spearman" ## ----sincellclust------------------------------------------------------------- sincellInfo(toyGEMset, "clust.method") <- "k-medoids" ## ----genMon, echo=TRUE, results='hide', message=FALSE------------------------- # Normally monocle will generate an internal warning for a condition with # length > 1. If your R environment has the _R_CHECK_LENGTH_1_CONDITION_ set # to verbose and/or abort, this will raise an error if(!any(c("abort","verbose") %in% Sys.getenv("_R_CHECK_LENGTH_1_CONDITION_"))){ toyGEMset <- generate_tree(dataSet = toyGEMset, treeType = "monocle") } ## ----monPlots, echo=FALSE, out.width="400px", message=FALSE------------------- if(!any(c("abort","verbose") %in% Sys.getenv("_R_CHECK_LENGTH_1_CONDITION_"))){ plotOriginalTree(toyGEMset, "monocle") } ## ----genSin, message=FALSE---------------------------------------------------- toyGEMset <- generate_tree(dataSet = toyGEMset, treeType = "sincell") ## ----sincellPlots, echo=FALSE, out.width="400px", message=FALSE--------------- plotOriginalTree(toyGEMset, "sincellIMC") plotOriginalTree(toyGEMset, "sincellMST") plotOriginalTree(toyGEMset, "sincellSST") ## ----genTSCAN, echo=TRUE, message=FALSE--------------------------------------- toyGEMset <- generate_tree(dataSet = toyGEMset, treeType = "TSCAN") ## ----TSCANplots, echo=FALSE, out.width="400px", message=FALSE----------------- plotOriginalTree(toyGEMset, "TSCANclustering") plotOriginalTree(toyGEMset, "TSCANsingleGene") ## ----getNames, echo=TRUE------------------------------------------------------ names(originalTrees(toyGEMset)) ## ----plotTree, echo=TRUE, message=FALSE--------------------------------------- plotOriginalTree(toyGEMset, "sincellIMC") ## ----save, eval = TRUE-------------------------------------------------------- save(toyGEMset, file = "toyGEMset.Rda") ## ----------------------------------------------------------------------------- sessionInfo()