microbiomeViz -- An R package for visualizing microbiome data

Authors:

Chenhao Li, Guangchuang Yu, Chenghao Zhu

Description:

• parse taxonomic profiling table
• GraPhlAn like tree visualization and annotation
• support cladograme visualization from phyloseq objects and .biom files

Showcase:

Example:

Install:

{r}
## run the following command first if you don't have ggtree installed.
setRepositories(ind=1:2)
devtools::install_github("lch14forever/microbiomeViz")

Parse a MetaPhlAn table

{r}
library(microbiomeViz)
data("SRS014459Stoolprofile")
tr <- parseMetaphlanTSV(SRS014459Stoolprofile)

Create a backbone

{r}
p <- tree.backbone(tr)
p

Add annotation

{r}
anno.data <- data.frame(node=c("gRoseburia", "cClostridia", "s_Bacteroidesovatus"),
                       color='red', stringsAsFactors = FALSE)
p <- clade.anno(p, anno.data)
p

From phyloseq objects

{r}
library(phyloseq)
data("GlobalPatterns")
GP = GlobalPatterns
GP = transformsamplecounts(GlobalPatterns, function(otu) otu/sum(otu)) GP = filter_taxa(GP, function(x) max(x)>=0.01,TRUE) GP = fixduplicatetax(GP)
tr = parsePhyloseq(GP) p = tree.backbone(tr, size=1)

From .biom files

The phyloseq package can import the otu table from .biom files.

{r}
richdensebiom  = system.file("extdata", "richdenseotu_table.biom",  package="phyloseq")
richdense = importbiom(richdensebiom, parseFunction=parsetaxonomygreengenes)
tr = parsePhyloseq(rich_dense)
p = tree.backbone(tr, size=1)