/usr/lib/R/site-library/phyloseq/doc/phyloseq-FAQ.R is in r-bioc-phyloseq 1.22.3-1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 | ## ---- 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()
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