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

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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

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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)