plot_boxplot: Boxplot for SummarizedPhyloseq data

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

Description

This function uses the ggplot2 package to generate a boxplot from a givin SummarizedPhyloseq-class object by specifying a taxon name.

Usage

plot_boxplot(spy, level, taxon, x, rows, cols, line, color, ...)

Arguments

spy	SummarizedPhyloseq-class
level	character. The phylogenic level.
taxon	character. The taxon name to plot.
line	character. A sample meta-data variable. If specified, geom_line will be called to draw lines between 2 points. This is particually usful to deal with repeated measures.
by	character. The sample meta-data variable to plot the abundance data againt to. It must be from the sample data's column names. If multiple variables are givin, facets will be used. The default is sample name. See examples.
color.by	character. A sample meta-data variable. If specified, points with different levels will be colored diffently. See examples.
jitter	numeric. If specified, points will be jittered. Recommanded value: 0.15. the line and jitter can not be specified at the same time.
point.size	numeric. The size of points. Default is 3
point.alpha	numeric. The transparency of points.
point.color	character. If the color.by is not specified, this value will be given the to the points color.
whisker.width	numeirc. The width of boxplot whisker. Default is 0.5.
color.pal	character. The color panel to use.
show.legend	logical. Whether to show legend. Default is TRUE.
syle	character. The pre-defined style to apply on the plot. "bw" is a empty default style using the theme_bw. "academic" is a classic style based on the theme_classic.
plotly	logical. If TRUE, a plotly variable will be returned.

Author(s)

Chenghao Zhu

Examples

data(fatigue)
fatigue = transform_sample_counts(fatigue, function(x) x/sum(x))
spy = summarizeFromPhyloseq(fatigue)
plot_box(spy, level = "Genus", taxon = "g__Ruminococcus", by = "Subject", jitter = 0.15)
plot_box(spy, level = "Genus", taxon = "g__Ruminococcus", by = c("Subject","Sex"), box.size = 1, whisker.size = 1, show.points = F, style = "academic")
plot_box(spy, level = "Genus", taxon = "g__Ruminococcus", by = c("Subject","Sex"), jitter = 0.15, box.size = 1, whisker.size = 1, point.alpha = 0.75, point.color = "steelblue", style = "academic")

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