R help - Mar 2009 - Working up examples of barplots with customized marginal items

Hello, everybody:

I'm back to share a long piece of example code.  Because I had trouble
understanding the role of par() and margins when customizing barplots,
I have struggled with this example.  In case you are a student wanting
to place legends or textual markers in the outer regions of a barplot,
you might run these examples.

There are a few little things I don't quite understand.

If you look below where I've below placed ???????,  you see I've used
text() to write inside the bars of a plot. To vertically align the
strings, I use the text() function's option pos.  However, the text is
not centered horizontally inside the bars. I don't think I found a
perfectly general solution with offset because it does not take into
account the width of the bars.

Second, can  changes to par be forced on all devices? I learned the
hard way that a change like par(mar=c(10,3,4,5)) will apply to the
current working device, but when a new output device is created, the
margins are re-set to default.  The margins in the saved graph won't
match the screen unless par is run again:

postscript( ---whatever--- )
###par must be run again to manipulate the postscript device:
par ( --whatever ---)
plot (--whatever---)
dev.off()

On the other hand,

dev.copy(postscript, ---whatever--)

will inherit the par values set on the screen device.

Is there a single command that can adjust the margins of all devices
that are created within a given session?


Anyway, here's my big barplot script and I hope some students benefit
from experimenting with it

pj

### Paul Johnson
### Twisting the margins of a barplot

### I never thought too much about customizing barplots, but
### now I have learned some tricks to share.  Step through these
### examples to see the possibilities.

set.seed(424242)

x <- rpois(10, lambda=10)

mynames <- c(rep("Really Long Name",9),"Really Long Name Long
Long")


#RSiteSearch("barplot names margins")


barplot(x)


### Note long names off edge:
barplot(x, names=mynames, las=2)

### Abbreviate offers one solution
barplot(x, names=abbreviate(mynames), las=2)

### Other option is to reset margins
###default mar is c(5.1, 4.1, 4.1, 2.1)

### Lets make the bottom margin larger
par(mar=c(15,4.1,4.1, 2.1))
barplot(x, names=mynames, las=2)



### Now the bottom is finished. But I'd like a legend.

legend("topleft", legend=c("A really long
label","B","Cee What I can
do?","D"), col=1:2)

### My bar hits the legend. How to fix?


### It is not sufficient to simply "move the legend" up
### because then it runs off the edge of the graph
barplot(x, names=mynames, las=2)
legend(2,22, legend=c("A really long label","B","Cee
What I can
do?","D"), col=1:2)

### By itself, changing the top margin does not help.
### It is also vital to set the xpd parameter to T so that
### R will draw outside the main plot region
par(mar=c(10,4.1,8.1, 2.1))
par(xpd=T)
barplot(x, names=mynames, las=2)
legend(2,22, legend=c("A really long label","B","Cee
What I can
do?","D"), col=1:2)


### Now lets gain some control on the colors and bars
### The default colors are so dark.  You can't write on top
### of them.  You can grab shades of gray like "gray30" or such.

### I'll just specify 4 colors I know will work. I prefer
### the light gray colors because they can be written over.
mycols <-
c("lightgray","gray70","gray80","gray90","gray75")

barplot(x, names=mynames, las=2, col=mycols)

legend(2,20,legend=c("A","B","C","D"),fill=mycols)

### Still, I don't like the solid shades so much.
### fill up the bars with angled lines.
### density determines number of lines inside the bar.

myden <- c(60,20,30,40,25)
### angles determines the direction of lines inside bars
myangles <- c(20,-30,60,-40,10)

barplot(x, names=mynames, las=2, col=mycols,density=myden,angle=c(20,60,-20))

legend(1,20,legend=c("A","B","C","D"),density=myden,angle=myangles)

### for my coupe de grace, lets do some writing in the bars.

### Recall from Verzani you can get the x coordinates from the barplot
barPositions <- barplot(x, names=mynames, las=2,
col=mycols,density=myden,angle=c(20,60,-20))

barPositions

### The text option srt=90 turns the text sideways

### I'm just guessing that bars 1 and 8 should be labeled
### at coordinates 5 and 5

text (barPositions[1], 5, "my first bar is great", srt=90)

text (barPositions[8], 5, "but 8 is greater", srt=90)

### Recently I had the problem of drawing a "clustered" bar chart.
### Lets suppose our x variable really represents responses from
### 2 groups of respondents, Men and Women.

## Create the matrix
xmatr <- matrix(x, nrow=5)

### Use beside=T to cause barplot to treat each column
### of values as a group
barplot(xmatr, beside=T, names=c("Men","Women"))

valueNames <- c("Very Strong","Somewhat Strong","Not
Strong","Somewhat
Weak","Very Weak")

### Use mtext to write in the margin so that labels on plot are nice.

par(mar=c(10,4.1,5.1, 2.1))

bp <- barplot(xmatr, beside=T, names=NULL)

### bp contains the positions of the bars.
mtext(valueNames, side=1, las=3, at=bp)

mtext(c("Men","Women"), side=1, at=c(bp[3],bp[8]),line=8,
cex=2)

### Adding numbers to the bars may clarify
text ( bp, as.vector(xmatr), labels=as.vector(xmatr),pos=1)

### However, the default color is too dark.

### Retrieve the first 5 items from the default grey color scale

gc <- grey.colors(5)

### Replace the first one with a lighter gray

gc[1] <- "gray80"

bp <- barplot(xmatr, beside=T, names=NULL, col=gc)

### bp contains the positions of the bars.
mtext(valueNames, side=1, las=3, at=bp)

mtext(c("Men","Women"), side=1, at=c(bp[3],bp[8]),line=8,
cex=2)

### Adding numbers to the bars may clarify
text ( bp, as.vector(xmatr), labels=as.vector(xmatr),pos=1)

### That's OK for me.  I wonder if I might not just write inside the
### bars. Hmmm.


bp <- barplot(xmatr, beside=T, names=c("Men","Women"),
col=gc)

text(bp, 0.5*as.vector(xmatr), valueNames, srt=90)

### Hm. That's OK, but maybe I'd pref uniform vertical
### placement of text.

bp <- barplot(xmatr, beside=T, names=c("Men","Women"),
col=gc)

text(bp, 2, valueNames, srt=90, pos=4)

### Hell, now the text is aligned vertically, but not centered
### in the bar. I can't figure out all of the details concerning
###

### I'm not able to say for sure what the best fix might be.
### I can either manipulate the x placement like so

bp <- barplot(xmatr, beside=T, names=c("Men","Women"),
col=gc)
text(bp-0.25, 2, valueNames, srt=90, pos=4)

### Or use the offset option in the text command.
### I do not understand why this particular value works.

bp <- barplot(xmatr, beside=T, names=c("Men","Women"),
col=gc)
text(bp, 2, valueNames, srt=90, pos=4, offset=-0.15)


### Don't forget: When save this into a file, the graph
### may be re-sized and text might "overflow" the boxes.
### That's especially likely if you have a large graph
### on the screen and then try to save the file with
### dev.copy(postscript...)
### That will resize some things, but not all.

### Here is the way to protect yourself.  Resize your "screen" device
### so that it is the same size--in inches--as the output file.

### On linux, I run

x11( width=6, height=6 )

### On windows, I think it is windows( width=6, height=6 )

### After you do that, run the par command again. The par command
### has to be executed again each time a device is created. That applies to
### the most recently created device.

p <- barplot(xmatr, beside=T, names=c("Men","Women"),
col=gc)
text(bp-0.25, 2, valueNames, srt=90, pos=4)

### If that looks OK, then do this


postscript(file="mybar-1.eps",height=6, width=6, onefile=F,
horizontal=F, paper="special",family="Times")
p <- barplot(xmatr, beside=T, names=c("Men","Women"),
col=gc)
text(bp-0.25, 2, valueNames, srt=90, pos=4)
dev.off()


### note that the par settings have shifted back to the defaults.
### Each device is separate.
### As a result, the barplot we created before with large margins would
### make a horrible plot if you forgot to insert the par() commands here:


postscript(file="mybar-2.eps",height=6, width=6, onefile=F,
horizontal=F, paper="special",family="Times")
par(mar=c(10,4.1,5.1, 2.1))


bp <- barplot(xmatr, beside=T, names=NULL, col=gc)

### bp contains the positions of the bars.
mtext(valueNames, side=1, las=3, at=bp)

mtext(c("Men","Women"), side=1, at=c(bp[3],bp[8]),line=8,
cex=2)

### Adding numbers to the bars may clarify
text ( bp, as.vector(xmatr), labels=as.vector(xmatr),pos=1)
dev.off()


### Finally, suppose you make a mistake of specifying your
### output device size too small. The graph I made before
### with the text in the bars looked good on the screen,
### but it looks bad in a smaller output device. The text
### does not match the bars in this example.

postscript(file="mybar-4.eps",height=4, width=4, onefile=F,
horizontal=F, paper="special",family="Times")
bp <- barplot(xmatr, beside=T, names=c("Men","Women"),
col=gc)
text(bp-0.25, 2, valueNames, srt=90, pos=4)
dev.off()
-- 
Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas