catplot: Correspondence at the top (CAT) plot
In drmjc/mjcgraphics: mjc's graphics library

Description Usage Arguments Details Value Note Author(s) References See Also

CAT plots are a useful way of comparing 2 lists, over a dynamic range of ‘top N’ thresholds.

  catplot(x, y, sizes = 1:length(x), sketch = 0.1,
    main = "CAT plot", ylim = c(0, 1), add = FALSE,
    proportion = FALSE, xTrue = rep(TRUE, length(x)),
    yTrue = rep(TRUE, length(y)), pch = NULL, ...)

`x`	usually a character vectors, but could be a vector of distinct numbers.
`y`	usually a character vectors, but could be a vector of distinct numbers.
`sizes`	an integer vector to use as the values for “n”
`sketch`	a value in (0,1.0] to be used if there are > 1000 datapoints
`main`	see `plot`
`ylim`	see `plot`
`add`	see `plot`
`proportion`	logical: set x-axis to proportion in common
`xTrue`	logical vector, same length as “x” to indicate significance of values in “x”
`yTrue`	logical vector, same length as “y” to indicate significance of values in “y”
`pch`	the print character. Default: NULL = choose the pch based on the values for xTrue and yTrue. see Details
`...`	arguments passed to plot

xTrue, yTrue and pch
Often, some of the x and y values also have a measure of statistical significance, or interest, and it would be nice to know at which point along the resulting plot that (a) both x and y were statistically significant (b), when neither are significant, and (c), where just x or y is significant. if pch=NULL, and xTrue and yTrue contain a range of TRUE and FALSE, then: if xTrue & yTrue, pch = 19 = filled circle if xTrue | yTrue, pch = 1 = open circle if !xTrue & !yTrue, pch = 2 = open triangle

none. makes a plot.

To create a CAT plot we made a list of n candidate genes for each of the two procedures and plotted the proportion of genes in common against the list size n (Irizarry et al, Nature Methods 2, 345 - 350 (2005)) sketch: in [0,1]. if < 1 then only a subset of points will be plotted when the sets are larger than 1000 values to compare. ie, if sketch=0.1, then only 10% of the data points in 1001:end will be plotted. This over-rides the sizes paramter. Set it to 1.0 to ignore it.

Mark Cowley, 29 August 2006

Irizarry et al, Nature Methods 2, 345 - 350 (2005)

calc.CAT catplot.vs.random

drmjc/mjcgraphics documentation built on May 15, 2019, 2:40 p.m.