Polishing my geom_bar for publication

Sun, Dec 4, 2011 9:37 AM

Sorry Dennis,
Didn't realized I went off the list!
I found a solution for one of my problem: removing x-axis label!

with this code: ggplot(Final2, aes(x=spp, y=WPUE, fill=season)) + geom_bar(position=position_dodge()) + geom_errorbar(aes(ymin=WPUE-wpue.se, ymax=WPUE+wpue.se),  size=.3,width=.2,position=position_dodge(.9)) + scale_x_discrete("", breaks=c("102","90","91","94","96"), labels= rep("", 5)) + ylab("Biomass (Weight (kg)/tow)") + scale_fill_grey(name="Survey season", breaks=c("summer", "winter"), labels=c("Spring", "Fall"))+ coord_flip() + theme_bw() + opts(axis.title.x = theme_text(size = 10), panel.grid.minor = theme_blank())

However, I am still trying to figure out how to fix the width of my two plots on my final pdf. I would appreciate any help on this! Thank you.

On 2011-12-04, at 12:59 PM, Aurelie Cosandey Godin wrote:

Thank you Denis,

I changed my code as you suggested, however the "xlab" didn't work & I tried something else (see below my new code), but I still get my labels for my x-axis (coord_flip) in my b figure ("spp" 96, 94, 91, etc...). See figure below.
To answer your question, I would like that both of my figure a & b have the same width on the final pdf. Right now they aren't because of the legend.

and (3) fix the width, such that both figures

have the same appearance regardless of the legend.

I'm afraid I don't understand clearly what you mean my 'same
appearance'. Could you provide a reproducible example, which includes
(possibly fake) data as well as code?



Here's my new code:

(a<- ggplot(Final2, aes(x=spp, y=CPUE, fill=season)) +
geom_bar(position=position_dodge()) +
geom_errorbar(aes(ymin=CPUE-cpue.se, ymax=CPUE+cpue.se),
 size=.3,                    width=.2,
position=position_dodge(.9)) +    scale_x_discrete("Species",
breaks=c("102","90","91","94","96"),
labels=c("SPINYTAIL","THORNY","SMOOTH","DEEPWATER","JENSEN'S")) + ylab("Abundance (fish/tow)")  + coord_flip() +
 scale_fill_grey() + theme_bw() + opts(axis.title.x =
theme_text(size = 10), panel.grid.minor = theme_blank(),
legend.position='none') )

##I added scale_x_discrete(NULL, breaks=c("102","90","91","94","96"), labels= rep(NULL, 5)) thinking that this would be able to remove my x-axis label (coord_flip) but it didn't... any other ideas of how I can achieve this?

(b<- ggplot(Final2, aes(x=spp, y=WPUE, fill=season)) + geom_bar(position=position_dodge()) + geom_errorbar(aes(ymin=WPUE-wpue.se, ymax=WPUE+wpue.se),  size=.3,width=.2,position=position_dodge(.9)) + scale_x_discrete(NULL, breaks=c("102","90","91","94","96"), labels= rep(NULL, 5)) + ylab("Biomass (Weight (kg)/tow)") + scale_fill_grey(name="Survey season", breaks=c("summer", "winter"), labels=c("Spring", "Fall"))+ coord_flip() + theme_bw() + opts(axis.title.x = theme_text(size = 10), panel.grid.minor = theme_blank()) )

pdf("polishing-layout3.pdf", width = 10, height = 6)
grid.newpage()
pushViewport(viewport(layout = grid.layout(1, 2)))
vplayout <- function(x, y)
 viewport(layout.pos.row = x, layout.pos.col = y)
print(a, vp = vplayout(1, 1))
print(b, vp = vplayout(1, 2))
dev.off()

<PastedGraphic-2.pdf>

Thank you very much!
Aurelie

On 2011-12-04, at 11:33 AM, Dennis Murphy wrote:

Hi:

On Sun, Dec 4, 2011 at 5:21 AM, Aurelie Cosandey Godin <GodinA at dal.ca> wrote:

Dear list,

I am new with ggplot2 and I have spend quiet some time putting together the
following code to create the attached plot. However there's still a few
things that I'm having trouble with!
I would be grateful if someone can tell me how to fix (1) the colour of my
bars into grey scales

One way is to provide greyscale values to scale_fill_discrete; e.g.,
   values = c("grey50","grey20")

(2) removing the y-axis (species name) on the right
figure to avoid duplication,

In the second figure, insert either
  ylab("")
or if you have a labs() statement that defines several titles at once,
  labs(..., y = "", ...)

and (3) fix the width, such that both figures

have the same appearance regardless of the legend.

I'm afraid I don't understand clearly what you mean my 'same
appearance'. Could you provide a reproducible example, which includes
(possibly fake) data as well as code?

Dennis

Thank you very much in advance!

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The code is as follow:


(a<-ggplot(Final2, aes(x=spp, y=CPUE, fill=season)) +
   geom_bar(position=position_dodge()) +
   geom_errorbar(aes(ymin=CPUE-cpue.se, ymax=CPUE+cpue.se),
                 size=.3,
                 width=.2,
                 position=position_dodge(.9)) +
   xlab("Species") +
scale_x_discrete(breaks=c("100","102","107","88","90","91","92","93","94","96","98","99"),
labels=c("WINTER","SPINYTAIL","BIGELOW'S","SKATES
(NS)","THORNY","SMOOTH","ABYSSAL","LITTLE","DEEPWATER","JENSEN'S","WHITE","SOFT"))
+
   ylab("Abundance (fish/tow)")  + coord_flip() +
   theme_bw() + opts(axis.title.x = theme_text(size = 10)) +
opts(panel.grid.minor = theme_blank()) + opts(legend.position='none') )

(b<-ggplot(Final2, aes(x=spp, y=WPUE, fill=season)) +
   geom_bar(position=position_dodge()) +
   geom_errorbar(aes(ymin=WPUE-wpue.se, ymax=WPUE+wpue.se),
                 size=.3,
                 width=.2,
                 position=position_dodge(.9)) + xlab(NULL)+
scale_x_discrete(breaks=c("100","102","107","88","90","91","92","93","94","96","98","99"),
labels=c("WINTER","SPINYTAIL","BIGELOW'S","SKATES
(NS)","THORNY","SMOOTH","ABYSSAL","LITTLE","DEEPWATER","JENSEN'S","WHITE","SOFT"))+
   ylab("Biomass (Weight (kg)/tow)") + scale_fill_hue(name="Survey season",
# Legend label, use darker colors
                  breaks=c("summer", "winter"),
                  labels=c("Spring", "Fall")) + coord_flip() +
   theme_bw() + opts(axis.title.x = theme_text(size = 10)) +
opts(panel.grid.minor = theme_blank()))

pdf("polishing-layout2.pdf", width = 10, height = 6)
grid.newpage()
pushViewport(viewport(layout = grid.layout(1, 2)))
vplayout <- function(x, y)
 viewport(layout.pos.row = x, layout.pos.col = y)
print(a, vp = vplayout(1, 1))
print(b, vp = vplayout(1, 2))
dev.off()


Aurelie Cosandey-Godin
Ph.D. student, Department of Biology
Industrial Graduate Fellow, WWF-Canada

Dalhousie University | Biology Dept. | 1459 Oxford Street |
Halifax, NS |
Canada
B3H 4R2

Phone: 1-902-494-2478 |
cell: 1-902-412-3404 |
Fax: 1-902-494-3736
Email: godina at dal.ca | Skype: aureliegodinco |
Web: wormlab.biology.dal.ca
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