Nothing
## ---- echo = FALSE------------------------------------------------------------
library(knitr)
opts_chunk$set(fig.width = 6, fig.height = 4)
## -----------------------------------------------------------------------------
library(adaptiveGPCA)
library(ggplot2)
library(phyloseq)
data(AntibioticPhyloseq)
theme_set(theme_bw())
## -----------------------------------------------------------------------------
pp = processPhyloseq(AntibioticPhyloseq)
## -----------------------------------------------------------------------------
out.agpca = adaptivegpca(pp$X, pp$Q, k = 2)
## -----------------------------------------------------------------------------
out.agpca
## -----------------------------------------------------------------------------
plot(out.agpca)
## -----------------------------------------------------------------------------
plot(out.agpca, type = "samples", axes = c(1,2))
plot(out.agpca, type = "variables", axes = c(1,2))
## ----eval = FALSE-------------------------------------------------------------
# inspectTaxonomy(out.agpca, AntibioticPhyloseq)
## ---- eval = FALSE------------------------------------------------------------
# out.ff = gpcaFullFamily(pp$X, pp$Q, k = 2)
# out.agpca = visualizeFullFamily(out.ff,
# sample_data = sample_data(AntibioticPhyloseq),
# sample_mapping = aes(x = Axis1, y = Axis2, color = type),
# var_data = tax_table(AntibioticPhyloseq),
# var_mapping = aes(x = Axis1, y = Axis2, color = Phylum))
## ----fig.width=7--------------------------------------------------------------
ggplot(data.frame(out.agpca$U, sample_data(AntibioticPhyloseq))) +
geom_point(aes(x = Axis1, y = Axis2, color = type, shape = ind)) +
xlab("Axis 1") + ylab("Axis 2")
## ----fig.width=9--------------------------------------------------------------
ggplot(data.frame(out.agpca$QV, tax_table(AntibioticPhyloseq))) +
geom_point(aes(x = Axis1, y = Axis2, color = Phylum)) +
xlab("Axis 1") + ylab("Axis 2")
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