documentation_default | R Documentation |
documentation_default
biom |
An rbiom object, such as from |
mtx |
A matrix-like object. |
tree |
A |
underscores |
When parsing the tree, should underscores be kept as
is? By default they will be converted to spaces (unless the entire ID
is quoted). Default |
md |
Dataset field(s) to include in the output data frame, or |
adiv |
Alpha diversity metric(s) to use. Options are: |
bdiv |
Beta diversity distance algorithm(s) to use. Options are:
|
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. |
ord |
Method for reducing dimensionality. Options are:
Multiple/abbreviated values allowed. Default: |
weighted |
Take relative abundances into account. When
|
normalized |
Only changes the "Weighted UniFrac" calculation.
Divides result by the total branch weights. Default: |
delta |
For numeric metadata, report the absolute difference in values
for the two samples, for instance |
rank |
What rank(s) of taxa to display. E.g. |
lineage |
Include all ranks in the name of the taxa. For instance,
setting to |
unc |
How to handle unclassified, uncultured, and similarly ambiguous taxa names. Options are:
Abbreviations are allowed. Default: |
other |
Sum all non-itemized taxa into an "Other" taxa. When
|
sparse |
If |
p.top |
Only display taxa with the most significant differences in
abundance. If |
y.transform |
The transformation to apply to the y-axis. Visualizing differences of both high- and low-abundance taxa is best done with a non-linear axis. Options are:
These methods allow visualization of both high- and low-abundance
taxa simultaneously, without complaint about 'zero' count
observations. Default: |
flip |
Transpose the axes, so that taxa are present as rows instead
of columns. Default: |
stripe |
Shade every other x position. Default: same as flip |
ci |
How to calculate min/max of the crossbar,
errorbar, linerange, and pointrange layers.
Options are: |
p.label |
Minimum adjusted p-value to display on the plot with a bracket.
If a numeric vector with more than one value is
provided, they will be used as breaks for asterisk notation.
Default: |
level |
The confidence level for calculating a confidence interval.
Default: |
caption |
Add methodology caption beneath the plot.
Default: |
outliers |
Show boxplot outliers? |
xlab.angle |
Angle of the labels at the bottom of the plot.
Options are |
k |
Number of ordination dimensions to return. Either |
split.by |
Dataset field(s) that the data should be split by prior to
any calculations. Must be categorical. Default: |
dm |
A |
groups |
A named vector of grouping values. The names should
correspond to |
df |
The dataset (data.frame or tibble object). "Dataset fields"
mentioned below should match column names in |
regr |
Dataset field with the x-axis (independent; predictive)
values. Must be numeric. Default: |
resp |
Dataset field with the y-axis (dependent; response) values,
such as taxa abundance or alpha diversity.
Default: |
stat.by |
Dataset field with the statistical groups. Must be
categorical. Default: |
color.by |
Dataset field with the group to color by. Must be
categorical. Default: |
shape.by |
Dataset field with the group for shapes. Must be
categorical. Default: |
facet.by |
Dataset field(s) to use for faceting. Must be categorical.
Default: |
colors |
How to color the groups. Options are:
See "Aesthetics" section below for additional information.
Default: |
shapes |
Shapes for each group.
Options are similar to |
patterns |
Patterns for each group.
Options are similar to |
test |
Method for computing p-values: |
fit |
How to fit the trendline. |
at |
Position(s) along the x-axis where the means or slopes should be
evaluated. Default: |
alt |
Alternative hypothesis direction. Options are |
mu |
Reference value to test against. Default: |
check |
Generate additional plots to aid in assessing data normality.
Default: |
within , between |
Dataset field(s) for intra- or inter- sample
comparisons. Alternatively, dataset field names given elsewhere can
be prefixed with |
seed |
Random seed for permutations. Must be a non-negative integer.
Default: |
cpus |
The number of CPUs to use. Set to |
permutations |
Number of random permutations to use.
Default: |
p.adj |
Method to use for multiple comparisons adjustment of
p-values. Run |
depths |
Rarefaction depths to show in the plot, or |
rline |
Where to draw a horizontal line on the plot, intended to show
a particular rarefaction depth. Set to |
clone |
Create a copy of |
labels |
Show sample names under each bar. Default: |
transform |
Transformation to apply. Options are:
|
ties |
When |
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