Cartesian {eudysbiome} | R Documentation |
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.
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"), ...)
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. |
log2 |
logical, specifying if x values should be log2 converted; default to |
micro.anno |
a character vector to annotate all row microbes in |
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 |
point.col |
a vector of colors for the points. |
point.alpha |
alpha value for points; see |
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 |
xaxis |
a character or expression vector specifying the labels of x axis by text; default to row names of |
yaxis |
a character or expression vector specifying the labels of y axis by axis; default to |
legend |
logical, specifying if the legend should be added to the plot; default to |
box |
logical, specifying if the quadrants should be highlighted by boxes; default to |
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 |
... |
additional parameters passed to the default method, or by it to |
The Cartesian plane plot
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)