create_annodata: Construct annotation table for microbiomeViz cladogram...

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

Description

It creats a annotation table base on a SummarizedPhyloStats object with node name and the color to highlight. This table can then be parsed to the clade.anno function from the microbiomeViz package. It goes through each slot in thee SummarizedPhyloStats object, and selects the taxa that matches the provided criteria. For example, the default setting selects all the taxa with a unadjusted pvalue small or equal to 0.05, and label the ones with a positive logFC as red, and negative as blue.

Usage

create_annodata(spys, coef = c("pvalue", "padj"), cutoff = 0.05,
  colors = c("#00468BFF", "#ED0000FF"), levels = 1:7)

Arguments

spys	(required) A SummarizedPhyloseq-class object.
coef	Must be pvalue or padj
cutoff	The coef cutoff for selection. Default is 0.05
colors	It takes a string vector of 2 colors. The first will be positive logFC and the second will be negativ.
levels	The phylogenic levels to annotate, with 1 being kingdom and 7 being species. Default is all levels.

See Also

SummarizedPhyloStats clade.anno

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