plotSingleFeature: Plot features

In zoecastillo/microbiomeExplorer: Microbiome Exploration App

Plot features

Description

This function plots the reads of a particular feature or set of features.

Usage

plotSingleFeature(
  aggdat,
  feature = "other",
  x_var = "SAMPLE_ID",
  ind = seq_len(10),
  plotTitle = NULL,
  ylab = "Reads",
  xlab = NULL,
  facet1 = NULL,
  facet2 = NULL,
  log = FALSE,
  showPoints = FALSE,
  fixedHeight = NULL,
  x_levels = NULL,
  pwidth = 500
)

Arguments

aggdat	aggregated MRExperiment
feature	Feature to plot.
x_var	Phenotype to aggregate over on X-axis. Default by "SAMPLE_ID".
ind	Indices of top abundant features to plot. Needed to determine appropriate color
plotTitle	Plot title. Default shows no title.
ylab	Y-axis label. Default is "Reads"
xlab	X-axis label. If NULL, x_var will be used as label.
facet1	Phenotype for facet 1.
facet2	Phenotype for facet 2.
log	Log2 transform data. Default is FALSE.
showPoints	add points for each sample on plot
fixedHeight	sets a specific plot height (differential analysis)
x_levels	restrict to specific levels of x_var (differential analysis)
pwidth	overall plot width; default is 650

Value

plotly plot object

Author(s)

Janina Reeder

Examples

data("mouseData", package = "metagenomeSeq")
aggdat <- aggFeatures(mouseData, level = "genus")
plotSingleFeature(aggdat, feature = "Prevotella", x_var = "diet")

zoecastillo/microbiomeExplorer documentation built on Sept. 11, 2022, 7:40 a.m.