## ----include=FALSE, echo=FALSE------------------------------------------------ # date: "`r doc_date()`" # "`r pkg_ver('BiocStyle')`" # ## ----echo=FALSE, results="hide", message=FALSE-------------------------------- require(knitr) opts_chunk$set(error=FALSE, message=FALSE, warning=FALSE) ## ----style, echo=FALSE, results='asis'---------------------------------------- BiocStyle::markdown() ## ----echo=FALSE, fig.cap="Feature-Sample data matrix", out.width = '100%'----- knitr::include_graphics("cytoSchematic.png") ## ----load-lib, message=FALSE-------------------------------------------------- library(cytoKernel) ## ----data-1, message=FALSE, warning=FALSE------------------------------------- data("cytoHDBMW") cytoHDBMW ## ----CytoK_output------------------------------------------------------------- library(cytoKernel) CytoK_output<- CytoK(cytoHDBMW,group_factor = rep(c(0, 1), c(4, 4)),lowerRho=2,upperRho=12,gridRho=4, alpha = 0.05,featureVars = NULL) CytoK_output ## Head of the data.frame containing shrunken effect sizes, shrunken ##effect size sd's, p values and adjusted p values head(CytoKFeatures(CytoK_output)) ## Head of the data.frame containing shrunken effect sizes, shrunken ##effect size sd's, p values and adjusted p values ordered by ##adjusted p values from low to high head(CytoKFeaturesOrdered(CytoK_output)) ## Percent of differentially expressed features CytoKDEfeatures(CytoK_output) ## ----byFeatures--------------------------------------------------------------- ## Filtering the data by reproducible features CytoKDEData_HD<- CytoKDEData(CytoK_output, by = "features") CytoKDEData_HD ## ----fig.cap="Differentially expressed (top 10) cluster-marker data using cytoKernel", plot-CytoK-Heatmap---- heatmap1<- plotCytoK(CytoK_output, group_factor = rep(c(0, 1), c(4, 4)),topK=10, featureVars = NULL) featureOrderedExtracted<- CytoKFeaturesOrdered(CytoK_output) rowmeta_cluster<- featureOrderedExtracted$cluster topK<- 10 rowmeta_clusterTopK<- rowmeta_cluster[seq_len(topK)] library(ComplexHeatmap) heatmap2<- Heatmap(rowmeta_clusterTopK, name = "cluster") heatmap2+heatmap1 ## ----session-info------------------------------------------------------------- sessionInfo()