Tools for visualising amplicon sequencing data.
To cite ampvis please use:
Albertsen M, Karst SM, Ziegler AS, Kirkegaard RH, Nielsen PH (2015) Back to Basics – The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities. PLoS ONE 10(7): e0132783. doi:10.1371/journal.pone.0132783
round
makes it possible to control the number of digits plotted (default: 1).tax.show
did not work with character input.plot.label.repel
and plot.nspecies.repel
adds ggrepel
functionality to aviod cluttering of points.plot.label.size
).plot.na
is now TRUE by default (@Kirk3gaard).order.x
now supports the input "cluster". Which will do basic hclust on the presented data and arrange it according to the clustering. amp_venn
generate venn diagrams of core species.color.vector
option (@Kirk3gaard).order.y
(@Kirk3gaard).sort.by
enables to show the x most abundant taxa from a specific group. Default option is to show the x most abundant taxa on average.min.abundance
option. The default value is now 0.1 which fixes the problems with log10 and 0 values.scale.seq
is now 100 by default. Like all other functions.amp_stats
can be used to generate a table with metadata, number of sequences and alpha-diversity indices.amp_rarecurve
can be used to generate rarefaction curves.scales
library as a dependency.tax.show
now correctly shows that 50 are displayed by default (@Kirk3gaard).calc
parameter (@Kirk3gaard).order.y
now supports the input "cluster". Which will do basic hclust on the presented data and arrange it according to the clustering.min.abundance
and max.abundance
can be used to limit the values displayed in the plot. This also impacts the new clustering option in order.y
.scale.seq
is now 100 by default. Hence, assuming that the data have been converted to a percentage.plot.group.manual
can now be used to group samples independently on the plot.color
option.group
now supports a vector of parameters.facet_wrap
.facet_wrap
.amp_function
, but can also be loaded manually using data(MiF)
.calc
option. Default is still mean.tax
option. adjust.zero
can be used to add a small constant to all OTU abundances that are 0 in order to display the correct median values when using log scales.plot.shape
can now be used to assign different shapes to points based on a sample variable.plot.theme
option that can be used to make publication friendly images fast.envfit.show
can be used to disable showing envfit vectors on the plot.plot.theme
option that can be used to make publication friendly images fast.plot.theme
option that can be used to make publication friendly images fast.plot.theme
option that can be used to make publication friendly images fast.data(MiDAS_1.20)
. It includes small updates to the taxonomy and a single sample have been removed (2591) due to wierdness. The OTU names are now locked! Hence, OTUs in this release will have the same name in the next release.data(DNAext_1.0)
.First release of the ampvis package
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