Plotting a taxonomic tree

Plots the taxonomic tree from a metabarlist object and maps an attribute onto it

ggtaxplot(metabarlist, taxo, sep.level, sep.info, thresh = NULL)

Arguments

metabarlist

a metabarlist object. Should contain taxonomic information in the `motus` table.

taxo

a character string or vector of strings indicating the name of the column (or group of columns) containing the full taxonomic information in the `motus` table from the metabarlist object.

sep.level

an optional character string to separate the terms. Required only if `taxo` is a string. NA not allowed.

sep.info

an optional character string to separate the terms. Required only if `taxo` is a string. NA not allowed.

thresh

a numeric indicating the relative abundance below which taxon labels won't be plotted

Value

a ggplot

Details

This function allows users to visualise the full taxonomic tree for a set of samples and to map attributes onto the produced tree (e.g. number of reads per node/branches, nb of MOTUs, etc.). The taxonomic information should follow a standard structure across samples (e.g. standard taxonomy as in Genbank, SILVA or BOLD or with defined taxonomic levels if `taxo` is a vector) by decreasing level of taxonomic resolution: the function does not infer missing taxonomic ranks. The taxonomic information should contain a level that is common to all MOTU taxonomic assignments (common ancestor).

See also

taxoparser

Author

Lucie Zinger

Examples

data(soil_euk)

# Using a taxonomic path

# \donttest{

## on all data. can take a while
ggtaxplot(soil_euk, "path", sep.level = ":", sep.info = "@")


## show only taxonomic labels if taxon has a relative abundance > 1e-3
ggtaxplot(soil_euk, "path", sep.level = ":", sep.info = "@", thresh = 1e-3)


# }

## run on a particular clade e.g. here arthropoda, otherwise difficult to read
arthropoda <- subset_metabarlist(soil_euk,
  table = "motus",
  indices = grepl("Arthropoda", soil_euk$motus$path)
)
#> Warning: Some PCRs in out have a number of reads of zero in table `reads`!
### plot
ggtaxplot(arthropoda, "path", sep.level = ":", sep.info = "@")



# Using a taxonomic table
taxo.col <- c(
  "phylum_name", "class_name", "order_name",
  "family_name", "genus_name", "species_name"
)
ggtaxplot(arthropoda, taxo.col)

## to do the same on the full soil_euk data,
# add a column "kingdom_name" with value "Eukaryota" in soil_euk$motus