## ----echo=FALSE--------------------------------------------------------------- knitr::opts_chunk$set( error=FALSE, warning=FALSE, message=FALSE, out.width='100%') library(BiocStyle) ## ----eval=!exists("SCREENSHOT"), include=FALSE-------------------------------- SCREENSHOT <- function(x, ...) knitr::include_graphics(x) ## ----------------------------------------------------------------------------- library(iSEEhex) ## ----------------------------------------------------------------------------- library(scRNAseq) # Example data ---- sce <- ReprocessedAllenData(assays="tophat_counts") class(sce) library(scater) sce <- logNormCounts(sce, exprs_values="tophat_counts") sce <- runPCA(sce, ncomponents=4) sce <- runTSNE(sce) rowData(sce)$ave_count <- rowMeans(assay(sce, "tophat_counts")) rowData(sce)$n_cells <- rowSums(assay(sce, "tophat_counts") > 0) sce ## ----------------------------------------------------------------------------- initialPanels <- list( ReducedDimensionPlot( ColorBy = "Feature name", ColorByFeatureName = "Cux2", PanelWidth = 6L), ReducedDimensionHexPlot( ColorBy = "Feature name", ColorByFeatureName = "Cux2", PanelWidth = 6L, BinResolution = 30) ) app <- iSEE(se = sce, initial = initialPanels) ## ----echo=FALSE--------------------------------------------------------------- SCREENSHOT("screenshots/reduced-dimension-hex-plot.png") ## ----------------------------------------------------------------------------- sessionInfo()