amp_heatmap: Generate a heatmap from amplicon data

In MadsAlbertsen/ampvis: Tools for visualising amplicon data

Description

Generate a heatmap in ggplot2 format from amplicon data in phyloseq format. Use sample metadata to aggregate samples and taxonomy to aggregate OTUs.

Usage

amp_heatmap(data)

Arguments

data	(required) A phyloseq object including sample data (or a list).
group	A variable from the associated sample data to group samples by.
normalise	A specific sample or group to normalise the counts to, or "relative".
scale	A variable from the associated sample data to scale the abundance by.
tax.aggregate	The taxonomic level that the data should be aggregated to (default: "Phylum")
tax.add	Additional taxonomic levels to display for each entry e.g. "Phylum" (default: "none")
tax.show	The number of taxa to show or a vector of taxa names (default: 10).
tax.class	Converts a specific phyla to class level instead (e.g. "p__Proteobacteria").
tax.empty	Either "remove" OTUs without taxonomic information, add "best" classification or add the "OTU" name (default: "best").
order.x	A taxonomy group or vector to order the x-axis by, alternatively "cluster".
order.y	A sample or vector to order the y-axis by, alternatively "cluster".
plot.numbers	Plot the values on the heatmap (default: T)
plot.breaks	A vector of breaks for the abundance legend.
plot.colorscale	Either "sqrt" or "log10" (default: "log10")
plot.na	Whether to color missing values with the lowest color in the scale (default: T).
scale.seq	The number of sequences in the pre-filtered samples (default: 100)
output	To output a plot or the complete data inclusive dataframes (default: "plot")
plot.text.size	The size of the plotted text (default: 4).
plot.theme	Chose different standard layouts choose from "normal" or "clean" (default: "normal").
calc	Calculate and display "mean", "max" or "median" across the groups (default: "mean").
min.abundance	All values below are given the same color (default: 0.1).
max.abundance	All values above are given the same color.
sort.by	Sort the heatmap by a specific value of the "group", e.g. "Treatment A".
color.vector	Vector with colors for colorscale e.g. c("red","white") (default: NULL)
round	Number of digits to plot (default: 1)

Value

A ggplot2 object or a list with the ggplot2 object and associated dataframes.

Author(s)

Mads Albertsen [e-mail]

MadsAlbertsen/ampvis documentation built on May 7, 2019, 2:08 p.m.