## ---- include=FALSE-------------------------------------------------------- library(BiocStyle) ## ---- eval=FALSE----------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("SEtools") ## ---- eval=FALSE----------------------------------------------------------- # devtools::install_github("plger/SEtools") ## -------------------------------------------------------------------------- suppressPackageStartupMessages({ library(SummarizedExperiment) library(SEtools) }) data("SE", package="SEtools") SE ## -------------------------------------------------------------------------- g <- c("Egr1", "Nr4a1", "Fos", "Egr2", "Sgk1", "Arc", "Dusp1", "Fosb", "Sik1") sehm(SE, genes=g) sehm(SE, genes=g, scale="row") ## -------------------------------------------------------------------------- sehm(SE, genes=g, scale="row", anno_rows="meanTPM") ## -------------------------------------------------------------------------- sehm(SE, genes=g, scale="row", anno_rows="meanTPM", gaps_at="Condition") ## -------------------------------------------------------------------------- lfcs <- assays(SE)$logcpm-rowMeans(assays(SE)$logcpm[,which(SE$Condition=="Homecage")]) rowData(SE)$cluster <- as.character(kmeans(lfcs,4)$cluster) sehm(SE, scale="row", anno_rows="cluster", toporder="cluster", gaps_at="Condition") ## -------------------------------------------------------------------------- crossHm( list(se1=SE, se2=SE), g, anno_colors = list( Condition=c( Homecage="green", Handling="orange", Restraint="red", Swim="blue") ) ) ## -------------------------------------------------------------------------- options("SEtools_def_hmcols"=c("white","grey","black")) ancols <- list( Condition=c( Homecage="green", Handling="orange", Restraint="red", Swim="blue" ) ) options("SEtools_def_anno_colors"=ancols) sehm(SE, g, do.scale = TRUE) ## -------------------------------------------------------------------------- se1 <- SE[,1:10] se2 <- SE[,11:20] se3 <- mergeSEs( list(se1=se1, se2=se2) ) se3 ## -------------------------------------------------------------------------- se3 <- mergeSEs( list(se1=se1, se2=se2), do.scale=FALSE) ## -------------------------------------------------------------------------- se3 <- mergeSEs( list(se1=se1, se2=se2), use.assays=c("counts", "logcpm"), do.scale=c(FALSE, TRUE)) ## ---- fig.cap="An example ggplot created from a melted SE.", fig.height=5---- d <- meltSE(SE, genes=g[1:4]) head(d) suppressPackageStartupMessages(library(ggplot2)) ggplot(d, aes(Condition, counts)) + geom_violin() + facet_wrap(~feature, scale="free") ## ----sessionInfo, echo=FALSE----------------------------------------------- sessionInfo()