Display taxa abundances as a stacked bar graph.
Usage
taxa_stacked(
biom,
rank = -1,
taxa = 6,
colors = TRUE,
patterns = FALSE,
label.by = NULL,
order.by = NULL,
facet.by = NULL,
dist = "euclidean",
clust = "complete",
other = TRUE,
unc = "singly",
lineage = FALSE,
xlab.angle = 90,
...
)
Arguments
- biom
An rbiom object, such as from
as_rbiom()
. Any value accepted byas_rbiom()
can also be given here.- rank
What rank(s) of taxa to display. E.g.
"Phylum"
,"Genus"
,".otu"
, etc. An integer vector can also be given, where1
is the highest rank,2
is the second highest,-1
is the lowest rank,-2
is the second lowest, and0
is the OTU "rank". Runbiom$ranks
to see all options for a given rbiom object. Default:-1
.- taxa
Which taxa to display. An integer value will show the top n most abundant taxa. A value 0 <= n < 1 will show any taxa with that mean abundance or greater (e.g.
0.1
implies >= 10%). A character vector of taxa names will show only those named taxa. Default:6
.- colors, patterns
A character vector of colors or patterns to use in the graph. A named character vector can be used to map taxon names to specific colors or patterns. Set to
TRUE
to auto-select colors or patterns, or toFALSE
to disable per-taxa colors or patterns. Default:colors=TRUE, patterns=FALSE
.- label.by, order.by
What metadata column to use for labeling and/or sorting the samples across the x-axis. Set
label.by='.sample'
to display sample names. Whenorder.by=NULL
, samples are arranged based ondist
andclust
, below. Default:label.by=NULL, order.by=NULL
.- facet.by
Dataset field(s) to use for faceting. Must be categorical. Default:
NULL
- dist, clust
Distance (
stats::dist()
) and clustering (stats::hclust()
) methods to use for automatically arranging samples along the x-axis to put samples with similar composition near one another. Default:dist="euclidean", clust="complete"
.- other
Sum all non-itemized taxa into an "Other" taxa. When
FALSE
, only returns taxa matched by thetaxa
argument. SpecifyingTRUE
adds "Other" to the returned set. A string can also be given to implyTRUE
, but with that value as the name to use instead of "Other". Default:FALSE
- unc
How to handle unclassified, uncultured, and similarly ambiguous taxa names. Options are:
"singly"
-Replaces them with the OTU name.
"grouped"
-Replaces them with a higher rank's name.
"drop"
-Excludes them from the result.
"asis"
-To not check/modify any taxa names.
Default:
"singly"
Abbreviations are allowed.- lineage
Include all ranks in the name of the taxa. For instance, setting to
TRUE
will produceBacteria; Actinobacteria; Coriobacteriia; Coriobacteriales
. Otherwise the taxa name will simply beCoriobacteriales
. You want to set this to TRUE whenunc = "asis"
and you have taxa names (such as Incertae_Sedis) that map to multiple higher level ranks. Default:FALSE
- xlab.angle
Angle of the labels at the bottom of the plot. Options are
"auto"
,'0'
,'30'
, and'90'
. Default:"auto"
.- ...
Parameters for underlying functions. Prefixing parameter names with a layer name ensures that a particular parameter is passed to, and only to, that layer.
Value
A ggplot2
plot.
The computed data points and ggplot
command are available as $data
and $code
,
respectively.
See also
Other taxa_abundance:
sample_sums()
,
taxa_boxplot()
,
taxa_clusters()
,
taxa_corrplot()
,
taxa_heatmap()
,
taxa_stats()
,
taxa_sums()
,
taxa_table()
Other visualization:
adiv_boxplot()
,
adiv_corrplot()
,
bdiv_boxplot()
,
bdiv_corrplot()
,
bdiv_heatmap()
,
bdiv_ord_plot()
,
plot_heatmap()
,
rare_corrplot()
,
rare_multiplot()
,
rare_stacked()
,
stats_boxplot()
,
stats_corrplot()
,
taxa_boxplot()
,
taxa_corrplot()
,
taxa_heatmap()