[R] graph woes

Patrick Jackson jackpat01 at gmail.com
Wed Jul 2 21:21:20 CEST 2008

Hey Gang,

Here is the situation.  First of all I am a newbie, in the arena of R,
so please bare with me.  I am trying to make a plot with a series of
plot lines that uses logs on the x axis, and when I plot it I am
having a few odd things go on that I do not know how to correct.

1.  the tick marks are not where I want them to be.  I want them at
.1, 1, 10, and 100, but I'm get them at 0.1, 0.5, 1.0, 5.0, 10.0,
50.0, 100.0
     a.  Also is there anyway to make sub tick marks?
2.  three of my curves are not coming out the way I want them to
     a.  one of my plot line when using standard axis, shows up, but
when I turn the log feature on for the x axis, it disappears, does
anyone know why?
     b.  I have two lines on this graph that are suppose to represent
perfect curves, but they are only showing the upper portions of the

On all of these I am assuming that there are easy resolutions, but
with me not knowing everything about R it isn't apparent to me what
the problems are.

Here is my code:

        png(imageFilename, width = 480, height = 360)
        par(cex = 0.75)
        plot(type = "s", y = control_Table, x = p_USER_Table, xlab =
"% of compound database searched", ylab = "% of known ligands found",
main = title , col = "#ff0000", pch = "20", xlim = (0.1, 100), ylim =
(0, 100), log = "x")
        axTicks(side = 1, log = True)
        points(type = "s", y = control_Table, x = p_PMF_Table, col = "#00c000")
        points(type = "s", y = control_Table, x = p_GOLD_Table, col = "#0080ff")
        points(type = "s", y = control_Table, x = p_CHEMSCORE_Table,
col = "#c000ff")
        points(type = "s", y = control_Table, x = p_AUTODOCK_Table,
col = "#00eeee")
        points(type = "s", y = control_Table, x = p_DOCK_Table, col = "#c04000")
        points(type = "s", y = control_Table, x = p_DFIRE_Table, col =
        lines(type = "l", x = control_Table, y = perfect_Table, col = "#2020c0")
        lines(type = "l", x = control_Table, y = control_Table, col = "#ffc020")
        legend("topleft", ["USER", "PMF", "GOLD", "CHEMSCORE",
"AUTODOCK", "DOCK", "DFIRE", "Perfect Ranking", "Random Ranking"], col
= ["#ff0000", "#00c000", "#0080ff", "#c000ff", "#00eeee", "#c04000",
"#eeee00", "#2020c0", "#ffc020"], lty = 1)

BTW if my code looks a bit odd it is because I am actually programing
through rpy, which is an interface that allows python to talk to R.

Thanks for all the help,

Patrick Jackson

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