Cartesian {eudysbiome} | R Documentation

## 2-D Cartesian plane Plots

### Description

This function plots a Cartesian plane of genus abundance difference across the tested conditions (y-axis) and their harmful/harmless nature (negative/positive x-axis), giving rise to up-utmost right and bottom-utmost left quadrants of microbial eubiotic impact and bottom-utmost right and up-utmost left quadrants of dysbiotic impact.

### Usage

    Cartesian(x,log2 = TRUE,micro.anno = NULL, comp.anno = NULL,
                 pch = 16, point.col = NULL,point.alpha = 0.6,ylim = NULL,
                 xlab = NULL,ylab = NULL,vlty = 2, hlty = 1, srt = 60,
                 font = 3, adj = c(1,1), xaxis = NULL, yaxis = NULL, legend = TRUE,
                 box = TRUE,box.col = c("darkblue","yellow"),
                 ...)

### Arguments

`x` | a data frame or numeric matrix of microbial abundance variations from which the plot is produced. Rows indicate the differential microbes, columns indicate the pair-wise conditions. `x` values can either be difference values or be log2 converted, specified with `log2` parameter.
`log2` | logical, specifying if x values should be log2 converted; default to `TRUE`.
`micro.anno` | a character vector to annotate all row microbes in `x`; e.g. `"harmless"`,`"harmful"`, should be in same length with the microbes. It can be given by the output of `microAnnotate`
`comp.anno` | a character vector of conditions pre-defined from the column pair-wise comparisons, should be in same length with the comparisons; default to the pair-wise comparisons.
`pch` | a vector of point types. Graphical parameters:see `par`.
`point.col` | a vector of colors for the points.
`point.alpha` | alpha value for points; see `adjustcolor`.
`ylim` | limits for the y axis.
`xlab` | a title for the x axis.
`ylab` | a title for the y axis.
`vlty, hlty` | types of vertical and horizontal lines to divide the plane with x-axis and y-axis, respectively.
`srt, font, adj` | graphical parameters for the text on x-axis, see `par`.
`xaxis` | a character or expression vector specifying the labels of x axis by text; default to row names of `x`.
`yaxis` | a character or expression vector specifying the labels of y axis by axis; default to `at` values in `axis`.
`legend` | logical, specifying if the legend should be added to the plot; default to `TRUE`.
`box` | logical, specifying if the quadrants should be highlighted by boxes; default to `TRUE`.
`box.col` | a vector of colors for the up-utmost right, bottom-utmost left quadrants and bottom-utmost right, up-utmost left quadrants, respectively; default to "darkblue" and "yellow". If only one color is specified, the other one can be `NA`.
`...` | additional parameters passed to the default method, or by it to `plot.window`, `text`,`mtext`,`axis`, and `title` to control the appearance of the plot.

### Value

The Cartesian plane plot

### Examples

    data(microDiff)
    attach(microDiff)

    newpar = par()
    par(mar = c(6,5.1,4.1,6))
    Cartesian(x = data,log2 = TRUE,micro.anno = micro.anno,pch = 16,
             comp.anno = comp.anno,point.col = c("blue","purple","orange"))

    par(newpar)
    detach(microDiff)

[Package eudysbiome version 1.17.0 Index]