![]() # loaded via a namespace (and not attached): # grid stats4 stats graphics grDevices utils datasets # LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C # LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 # LAPACK: /home/biocbuild/bbs-3.16-bioc/R/lib/libRlapack.so # BLAS: /home/biocbuild/bbs-3.16-bioc/R/lib/libRblas.so ![]() Library( "pasilla") pasCts 2, 8, 1)), labSize = 6.0, shape = c( 6, 6, 19, 16), title = "DESeq2 results", subtitle = "Differential expression", caption = bquote( ~Log ~ "fold change cutoff, 2 p-value cutoff, 10e-4"), legendPosition = "right", legendLabSize = 14, col = c( "gre圓0", "forestgreen", "royalblue", "red2"), colAlpha = 0.9, drawConnectors = TRUE, hline = c( 10e-8), widthConnectors = 0.5) p1 P1 2.5, 'gold', 'black')) lour <- 'black' names(lour) <- 'high' names(lour) <- 'mid' names(lour) <- 'low' p2 <- EnhancedVolcano(res, lab = rownames(res), x = 'log2FoldChange', y = 'pvalue', selectLab = rownames(res), xlab = bquote( ~Log ~ 'fold change'), title = 'Custom shape & colour over-ride', pCutoff = 10e-14, FCcutoff = 1.0, pointSize = 5.5, labSize = 0.0, shapeCustom = keyvals.shape, colCustom = lour, colAlpha = 1, legendPosition = 'right', legendLabSize = 15, legendIconSize = 5.0, drawConnectors = TRUE, widthConnectors = 0.5, colConnectors = 'grey50', gridlines.major = TRUE, gridlines.minor = FALSE, border = 'full', borderWidth = 1.0, borderColour = 'black') library(gridExtra) library(grid) grid.arrange(p1, p2, ncol= 2, top = textGrob( 'EnhancedVolcano', just = c( 'center'), gp = gpar( fontsize = 32)))
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