Paired boxplot (e.g. diversity, taxa abundances..)

[antagomir]

Add a method that facilitates handy visualization of paired samples on a box/jitterplot, pairs indicated by (coloured lines) as shown in the figure.

Tentative gists for

• taxa abundances
• alpha diversity

Current implementation depends on scater and needs to use colData also for assay data. If this can be simplified for a user, such method might have good use in exploratory data analysis.

Figure:

[antagomir]

After implementing this, an exampl could be added to miaTime vignettes?
microbiome/miaTime#61

[antagomir]

Also the plotAbundance function can be extended to provide grouped boxplots.

Something like:

library(mia)
library(ggplot2)
data(peerj13075)
tse <- peerj13075
df <- data.frame(t(assay(tse)))
df$Geographical_location <- factor(colData(tse)$Geographical_location)
ggplot(df, aes(x=Geographical_location, y=OTU2529)) + geom_boxplot()

But implemented like:

plotAbundance(tse, assay.type="counts", rank = "Phylum", group="Geographical_location", layout="bar")

-> But need to think if it is worth a dedicated wrapper like this.