corrPhenotype {microbiomeExplorer} | R Documentation

## Scatterplot of a feature and a phenotype

### 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")

[Package microbiomeExplorer version 1.4.0 Index]