plotLongFeature: Plot longitudinal features

In microbiomeExplorer: Microbiome Exploration App

Description

This function plots the reads of a particular feature over different time points.

Usage

plotLongFeature(
  aggdat,
  feature,
  x_var,
  id_var = "SAMPLE_ID",
  plotTitle = NULL,
  ylab = "Reads",
  log = FALSE,
  showLines = TRUE,
  fixedHeight = NULL,
  x_levels = NULL,
  pwidth = 650
)

Arguments

aggdat	aggregated MRExperiment
feature	Feature to plot.
x_var	Phenotype to show along on X-axis.
id_var	phenotype used to connect data points. Default is "SAMPLE_ID"
plotTitle	Plot title. Default shows no title.
ylab	Y-axis label. Default is "Reads"
log	Log2 transform data. Default is FALSE.
showLines	add lines between the points
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 object holding long feature plot

Author(s)

Janina Reeder, Mo Huang

Examples

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

microbiomeExplorer documentation built on Nov. 8, 2020, 8:16 p.m.