Melt phyloseq data object into large data.frame
The psmelt function is a specialized melt function for melting phyloseq objects
(instances of the phyloseq class), usually for producing graphics
with ggplot2. psmelt relies heavily on the
melt and merge functions.
The naming conventions used in downstream phyloseq graphics functions
have reserved the following variable names that should not be used
as the names of sample_variables
or taxonomic rank_names.
These reserved names are c("Sample", "Abundance", "OTU").
Also, you should not have identical names for
sample variables and taxonomic ranks.
That is, the intersection of the output of the following two functions
sample_variables, rank_names
should be an empty vector
(e.g. intersect(sample_variables(physeq), rank_names(physeq))).
All of these potential name collisions are checked-for
and renamed automtically with a warning.
However, if you (re)name your variables accordingly ahead of time,
it will reduce confusion and eliminate the warnings.
psmelt(physeq)
physeq |
(Required). An |
Note that
“melted” phyloseq data is stored much less efficiently,
and so RAM storage issues could arise with a smaller dataset
(smaller number of samples/OTUs/variables) than one might otherwise expect.
For common sizes of graphics-ready datasets, however,
this should not be a problem.
Because the number of OTU entries has a large effect on the RAM requirement,
methods to reduce the number of separate OTU entries –
for instance by agglomerating OTUs based on phylogenetic distance
using tip_glom –
can help alleviate RAM usage problems.
This function is made user-accessible for flexibility,
but is also used extensively by plot functions in phyloseq.
A data.frame-class table.
data("GlobalPatterns")
gp.ch = subset_taxa(GlobalPatterns, Phylum == "Chlamydiae")
mdf = psmelt(gp.ch)
nrow(mdf)
ncol(mdf)
colnames(mdf)
head(rownames(mdf))
# Create a ggplot similar to
library("ggplot2")
p = ggplot(mdf, aes(x=SampleType, y=Abundance, fill=Genus))
p = p + geom_bar(color="black", stat="identity", position="stack")
print(p)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.