## LinkedCharts for airways example library( DESeq2 ) library( airway ) library( rlc ) data( airway ) a <- AnnotationDbi::intraIDMapper( rownames(airway), species="HOMSA", srcIDType="ENSEMBL", destIDType = "SYMBOL" ) rownames(airway)[ match( names(a), rownames(airway) ) ] <- unlist(a) dds <- DESeqDataSet( airway, ~ cell + dex ) dds <- DESeq( dds ) res <- results( dds ) openPage( useViewer=FALSE, layout="table2x2" ) gene <- 1 lc_scatter( dat( x = res$baseMean, y = res$log2FoldChange, colour = ifelse( !is.na(res$padj) & res$padj < .1, "red", "black" ), label = rownames(res), on_click = function(k) { gene <<- k; updateCharts("A2") } ), size = 2, logScaleX = 10, domainY = c( -5, 5 ), place = "A1" ) lc_scatter( dat( x = colData(dds)$cell, y = 1+counts( dds, normalized=TRUE )[ gene, ], colourValue = colData(dds)$dex ), logScaleY = 10, place = "A2" )