plot_heatmap: Generate a heatmap with all the taxa the match a given...

In zhuchcn/phylox: Analyzing and Visualization Microbiome Data on Different Phylogenic Levels

Description

By specifying the phylogenic level, coeficient, and cutoff, all the taxa with a adjusted or unadjusted p value that is smaller than the cutoff will be selected. Then the summarized OTU table at the specifed level is extracted to generate a heatmap.

This function depends on the zheatmap package. The package can be installed from the github using devtools::install_github("zhuchcn/zheatmap")

Usage

plot_heatmap(spy, spys, level = "Genus", coef = "pvalue",
  cutoff = 0.05, anno.var, ...)

Arguments

spy	SummarizedPhyloseq object
spys	SummarizedPhyloStats object
level	character variable indicates the targeted phylogenic level
coef	character, either "pvalue" or "padj"
cutoff	numeric, the cutoff of coef to use
anno.var	character, indicates the sample metadata variabel to use for annotation as a side bar. It must be one from the colnames of the sample data.
...	other parameters supported by the zheatmap function.

Author(s)

Chenghao Zhu

See Also

SummarizedPhyloseq-class, SummarizedPhyloStats-class, zheatmap

Examples

data(fatigue)
fatigue = transform_sample_counts(fatigue, function(x) x/sum(x))
spy = summarizeFromPhyloseq(fatigue)
design = model.matrix(data = as(sample_data(fatigue), "data.frame"), ~Subject + 1)
spys_lm = spy_to_limma(spy_prop, design, transform = "log", p.value = 2, coef = 2)
plot_heatmap(spy,
             spys_lm,
             coef = "pvalue",
             cutoff = 0.1,
             anno.var = "Subject")

zhuchcn/phylox documentation built on May 31, 2019, 5:14 p.m.