This function is called automatically by OTUsummary() and also can be used separately to plot the results produced by OTUsummary() with more plotting options
summaryPlotOTU(data, xgroup, facet = NA, type = "bar",
x.order = NA, whiskers = "ci", otus = NA,log.base=10)A summary table generated by HPDplot(), it is the first element in the returned list.
Which factor will be used to form the x axis (for 2-way designs).
The factor by which the plot will be split into facets (for 2-way designs).
Two types are supported: "bar" and "line" ("line" also has points). "bar" is more useful to plot fold-changes returned when OTUsummary() is run with the option 'relative=TRUE'. "line" is better for plotting actual inferred OTU abundances across factor levels; it is particularly good for time courses and other cases when multiple factor levels must be compared to each other. "bar" is good to plot log(fold-changes) relative to global control.
A vector giving the order of factor levels on the x-axis. If unspecified, alphanumeric order will be used.
The interval indicated by the whiskers. Default is "ci", the 95% credible interval; another option is "sd" - standard deviation of the posterior.
Vector of OTU names to plot. By default, all OTUs in the summary will be plotted.
Base of the logarithm to indicate on the y-axis label.
A ggplot object. See http://docs.ggplot2.org/0.9.2.1/theme.html for ways to modify it, such as add text, rotate labels, change fonts, etc.
The function invokes ggplot() functon from the ggplot2 package to plot the results either as a single panel (one-way designs) or a multi-panel (2-way designs, one panel per level of the factor specified by 'facet' argument).
Elizabeth A. Green, Sarah W. Davies, Mikhail V. Matz, Monica Medina Next-generation sequencing reveals cryptic Symbiodinium diversity within Orbicella faveolata and Orbicella franksi at the Flower Garden Banks, Gulf of Mexico. PeerJ 2014 https://peerj.com/preprints/246/