## ---- warning=FALSE, message=FALSE-------------------------------------------- library("phyloseq"); packageVersion("phyloseq") library("ggplot2"); packageVersion("ggplot2") theme_set(theme_bw()) ## ----------------------------------------------------------------------------- data(esophagus) plot_tree(esophagus) ## ----------------------------------------------------------------------------- p1 = plot_tree(esophagus, color = "Sample") p1 p1 + ggtitle("This is my title.") + annotate("text", 0.25, 3, color = "orange", label = "my annotation") ## ----------------------------------------------------------------------------- data("esophagus") mdf = psmelt(esophagus) # Simple bar plot. See plot_bar() for more. ggplot(mdf, aes(x = Sample, y = Abundance)) + geom_bar(stat = "identity", position = "stack", color = "black") # Simple heat map. See plot_heatmap() for more. ggplot(mdf, aes(x = Sample, y = OTU, fill = Abundance)) + geom_raster()