R help - Dec 2011 - black and white in qplot? layout 4 graphs in one screen

Hello, 

I am trying to plot means and standard errors conditioned by a factor, using
qplot.  I am successful at getting the bar graph I want with a error bar,
however I have tried many things and cannot get the bars to change colors. 
Currently showing as red and blue, but need it to be black and white for
publication.  Any suggestions please?  

Using a data set June, which is str:
'data.frame':   21 obs. of  6 variables:
 $ BLCK     : Factor w/ 4 levels
"","B","I","W": 3 4 2 3 2 2 2 4 3 4 ...
 $ PLOT     : int  3 3 6 1 2 5 1 1 2 2 ...
 $ TRT      : Factor w/ 5 levels
"","crop","ten",..: 2 2 2 3 3 3 4 4 4 5 ...
 $ Date     : Factor w/ 8 levels ""," 6/16/11",..: 2 2 2 2 2
2 2 2 2 2 ...
 $ habitat  : Factor w/ 3 levels "","C","P": 2 2 2
2 2 2 2 2 2 2 ...
 $ Abundance: num  0.333 0 1.333 0 1.667 ...

Current code is: 

Ab.avg<-ddply(June, c("TRT", "habitat"), function(df)
 return(c(Ab.avg=mean(df$Abundance), Ab.sd=sd(df$Abundance))))

avg.plot<-qplot(TRT, Ab.avg, fill=factor(habitat), 
data=Ab.avg, geom="bar", position="dodge")

dodge <- position_dodge(width=0.9)
avg.plot++geom_linerange(aes(ymax=Ab.avg+Ab.sd, ymin=Ab.avg-Ab.sd),
position=dodge)+theme_bw()

http://r.789695.n4.nabble.com/file/n4223035/june_bar_graph.png 

Also, would like to plot 4 of these bar graphs (for four dates) on the same
screen, I cannot get the par() or layout() function to work with qplot.  Is
there another way?  

Thank you!

--
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On 21.12.2011 21:16, rachaelohde wrote:
> Hello,
>
> I am trying to plot means and standard errors conditioned by a factor,
using
> qplot.  I am successful at getting the bar graph I want with a error bar,
> however I have tried many things and cannot get the bars to change colors.
> Currently showing as red and blue, but need it to be black and white for
> publication.  Any suggestions please?
>
> Using a data set June, which is str:
> 'data.frame':   21 obs. of  6 variables:
>   $ BLCK     : Factor w/ 4 levels
"","B","I","W": 3 4 2 3 2 2 2 4 3 4 ...
>   $ PLOT     : int  3 3 6 1 2 5 1 1 2 2 ...
>   $ TRT      : Factor w/ 5 levels
"","crop","ten",..: 2 2 2 3 3 3 4 4 4 5 ...
>   $ Date     : Factor w/ 8 levels ""," 6/16/11",..: 2 2
2 2 2 2 2 2 2 2 ...
>   $ habitat  : Factor w/ 3 levels "","C","P":
2 2 2 2 2 2 2 2 2 2 ...
>   $ Abundance: num  0.333 0 1.333 0 1.667 ...
>
> Current code is:
>
> Ab.avg<-ddply(June, c("TRT", "habitat"),
function(df)
>   return(c(Ab.avg=mean(df$Abundance), Ab.sd=sd(df$Abundance))))
>
> avg.plot<-qplot(TRT, Ab.avg, fill=factor(habitat),
> data=Ab.avg, geom="bar", position="dodge")
>
> dodge<- position_dodge(width=0.9)
> avg.plot++geom_linerange(aes(ymax=Ab.avg+Ab.sd, ymin=Ab.avg-Ab.sd),
> position=dodge)+theme_bw()
>
> http://r.789695.n4.nabble.com/file/n4223035/june_bar_graph.png
>
> Also, would like to plot 4 of these bar graphs (for four dates) on the same
> screen, I cannot get the par() or layout() function to work with qplot.  Is
> there another way?
What is ddply and what is qplot?
If you find that out for yourself, please also tell on the list where 
you took those functions from. qplot is not on base R graphics, hence 
see the help page of the package you took that function from (assuming 
ggplot2).

Uwe Ligges




>
> Thank you!
>
> --
> View this message in context:
http://r.789695.n4.nabble.com/black-and-white-in-qplot-layout-4-graphs-in-one-screen-tp4223035p4223035.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

You might find the ggplot mailing list a friendlier place to ask
questions about ggplot2.
Hadley

On Wed, Dec 21, 2011 at 2:16 PM, rachaelohde <cox.rachael at gmail.com>
wrote:
> Hello,
>
> I am trying to plot means and standard errors conditioned by a factor,
using
> qplot. ?I am successful at getting the bar graph I want with a error bar,
> however I have tried many things and cannot get the bars to change colors.
> Currently showing as red and blue, but need it to be black and white for
> publication. ?Any suggestions please?
>
> Using a data set June, which is str:
> 'data.frame': ? 21 obs. of ?6 variables:
> ?$ BLCK ? ? : Factor w/ 4 levels
"","B","I","W": 3 4 2 3 2 2 2 4 3 4 ...
> ?$ PLOT ? ? : int ?3 3 6 1 2 5 1 1 2 2 ...
> ?$ TRT ? ? ?: Factor w/ 5 levels
"","crop","ten",..: 2 2 2 3 3 3 4 4 4 5 ...
> ?$ Date ? ? : Factor w/ 8 levels ""," 6/16/11",..: 2 2
2 2 2 2 2 2 2 2 ...
> ?$ habitat ?: Factor w/ 3 levels "","C","P":
2 2 2 2 2 2 2 2 2 2 ...
> ?$ Abundance: num ?0.333 0 1.333 0 1.667 ...
>
> Current code is:
>
> Ab.avg<-ddply(June, c("TRT", "habitat"),
function(df)
> ?return(c(Ab.avg=mean(df$Abundance), Ab.sd=sd(df$Abundance))))
>
> avg.plot<-qplot(TRT, Ab.avg, fill=factor(habitat),
> data=Ab.avg, geom="bar", position="dodge")
>
> dodge <- position_dodge(width=0.9)
> avg.plot++geom_linerange(aes(ymax=Ab.avg+Ab.sd, ymin=Ab.avg-Ab.sd),
> position=dodge)+theme_bw()
>
> http://r.789695.n4.nabble.com/file/n4223035/june_bar_graph.png
>
> Also, would like to plot 4 of these bar graphs (for four dates) on the same
> screen, I cannot get the par() or layout() function to work with qplot. ?Is
> there another way?
>
> Thank you!
>
> --
> View this message in context:
http://r.789695.n4.nabble.com/black-and-white-in-qplot-layout-4-graphs-in-one-screen-tp4223035p4223035.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.


-- 
Assistant Professor / Dobelman Family Junior Chair
Department of Statistics / Rice University
http://had.co.nz/

Hi,

On 22 December 2011 09:16, rachaelohde <cox.rachael at gmail.com>
wrote:
> Hello,
>
> I am trying to plot means and standard errors conditioned by a factor,
using
> qplot. ?I am successful at getting the bar graph I want with a error bar,
> however I have tried many things and cannot get the bars to change colors.
> Currently showing as red and blue, but need it to be black and white for
> publication. ?Any suggestions please?
Have a look at scale_fill_grey() and grid.arrange()

d= data.frame(x=sample(letters[1:4], 10, replace=TRUE), f=gl(2, 10))
( p = qplot(x, data=d, position="dodge", fill=f) + scale_fill_grey() )
library(gridExtra)
grid.arrange(p, p, p , p, ncol=2)

HTH,

baptiste
>
> Using a data set June, which is str:
> 'data.frame': ? 21 obs. of ?6 variables:
> ?$ BLCK ? ? : Factor w/ 4 levels
"","B","I","W": 3 4 2 3 2 2 2 4 3 4 ...
> ?$ PLOT ? ? : int ?3 3 6 1 2 5 1 1 2 2 ...
> ?$ TRT ? ? ?: Factor w/ 5 levels
"","crop","ten",..: 2 2 2 3 3 3 4 4 4 5 ...
> ?$ Date ? ? : Factor w/ 8 levels ""," 6/16/11",..: 2 2
2 2 2 2 2 2 2 2 ...
> ?$ habitat ?: Factor w/ 3 levels "","C","P":
2 2 2 2 2 2 2 2 2 2 ...
> ?$ Abundance: num ?0.333 0 1.333 0 1.667 ...
>
> Current code is:
>
> Ab.avg<-ddply(June, c("TRT", "habitat"),
function(df)
> ?return(c(Ab.avg=mean(df$Abundance), Ab.sd=sd(df$Abundance))))
>
> avg.plot<-qplot(TRT, Ab.avg, fill=factor(habitat),
> data=Ab.avg, geom="bar", position="dodge")
>
> dodge <- position_dodge(width=0.9)
> avg.plot++geom_linerange(aes(ymax=Ab.avg+Ab.sd, ymin=Ab.avg-Ab.sd),
> position=dodge)+theme_bw()
>
> http://r.789695.n4.nabble.com/file/n4223035/june_bar_graph.png
>
> Also, would like to plot 4 of these bar graphs (for four dates) on the same
> screen, I cannot get the par() or layout() function to work with qplot. ?Is
> there another way?
>
> Thank you!
>
> --
> View this message in context:
http://r.789695.n4.nabble.com/black-and-white-in-qplot-layout-4-graphs-in-one-screen-tp4223035p4223035.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.