## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----dependencies, warning=FALSE, message=FALSE------------------------------- library(ExperimentHub) library(bsseq) ## ----loading------------------------------------------------------------------ eh <- ExperimentHub() BS.obj.ex.fit <- eh[["EH1072"]] ## ----granges------------------------------------------------------------------ regions <- GRanges( seqnames = c("X"), ranges = IRanges(start = c(7579676), end = c(7595243) ) ) ## ----plotRegion--------------------------------------------------------------- plotRegion(BS.obj.ex.fit, region=regions[1,], extend = 2000) ## ----check_order-------------------------------------------------------------- colnames(BS.obj.ex.fit) ## ----plotRegionColor---------------------------------------------------------- pData <- pData(BS.obj.ex.fit) pData$col <- rep(c("red", "blue", "green", "yellow", "orange"), rep(3,5)) pData(BS.obj.ex.fit) <- pData plotRegion(BS.obj.ex.fit, region=regions[1,], extend = 2000) ## ----loading_group------------------------------------------------------------ BS.obj.ex.fit.combined <- eh[["EH1073"]] ## ----check_order_group-------------------------------------------------------- colnames(BS.obj.ex.fit.combined) ## ----plotRegionColor_group---------------------------------------------------- pData <- pData(BS.obj.ex.fit.combined) pData$col <- c("red", "blue", "yellow", "orange", "green") pData(BS.obj.ex.fit.combined) <- pData plotRegion(BS.obj.ex.fit.combined, region=regions[1,], extend = 2000) ## ----RNA-seq_loading---------------------------------------------------------- se_rpkms <- eh[["EH1074"]] ## ----RNA-seq_structure-------------------------------------------------------- head(assay(se_rpkms)) head(rowData(se_rpkms)) ## ----RNA-seq_foxp3------------------------------------------------------------ assay(se_rpkms)[rowData(se_rpkms)$id_symbol=="Foxp3",] ## ----RNA-seq_foxp3_colData---------------------------------------------------- head(colData(se_rpkms)) ## ----RNA-seq_foxp3_vis-------------------------------------------------------- library(ggplot2) library(reshape2) foxp3_rpkm <- assay(se_rpkms)[rowData(se_rpkms)$id_symbol=="Foxp3",] foxp3_rpkm_molten <- melt(foxp3_rpkm) ggplot(data=foxp3_rpkm_molten, aes(x=rownames(foxp3_rpkm_molten), y=value, fill=colData(se_rpkms)$tissue_cell)) + geom_bar(stat="identity") + theme(axis.text.x=element_text(angle=45, hjust=1)) + xlab("Sample") + ylab("RPKM") + ggtitle("FoxP3 expression") + guides(fill=guide_legend(title="tissue / cell type")) ## ----sessionInfo, echo=FALSE-------------------------------------------------- sessionInfo()