corrPhenotype: Scatterplot of a feature and a phenotype

In microbiomeExplorer: Microbiome Exploration App

Description

This function plots a scatterplot of a feature and a phenotype along with sample correlation statistics.

Usage

corrPhenotype(
  aggdat,
  feature,
  phenotype,
  log = TRUE,
  method = c("spearman", "pearson", "kendall"),
  addRegression = TRUE,
  col_by = NULL,
  facet1 = NULL,
  facet2 = NULL,
  plotTitle = "",
  xlab = NULL,
  ylab = NULL,
  allowWebGL = TRUE,
  pwidth = 550,
  pheight = 200
)

Arguments

aggdat	aggregated MRExperiment
feature	Feature input.
phenotype	Phenotype input (must be numeric)
log	Log2 transform data. Default is TRUE.
method	Correlation coefficient. One of "spearman" (default), "pearson", or "kendall".
addRegression	boolean parameter indicating whether linear regression line should be drawn; default: TRUE
col_by	Phenotype for coloring.
facet1	Phenotype for facet 1.
facet2	Phenotype for facet 2. (WIP/TODO)
plotTitle	Plot title. Default is no title.
xlab	X-axis label. Default is feat1.
ylab	Y-axis label. Default is feat2.
allowWebGL	boolean indicating if WebGL should be used for large data
pwidth	overall plot width; default is 550
pheight	overall plot height; default is 200

Value

list holding plotly plot and lm fit

Examples

data("mouseData", package = "metagenomeSeq")
aggdat <- aggFeatures(mouseData, level = "genus")
corrPhenotype(aggdat, feature = "Bacteroides", phenotype = "relativeTime")

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