[R] Sciplot: Increasing the width of bargraph and decreasing the sapce b/n groups

[Jim Lemon]

On 05/06/2014 05:02 AM, Roopa Subbaiaih wrote:
> Hello,
>
> I am trying to plot bargraphs susing Sciplot. Is there a way to increase
> the width of the bar graphs and decrease the space b/n the groups? I am
> pasting the script as well as attaching the graph.
>
> Bio6<- read.csv("Data/Plin1.csv",na.strings="",header=T)
> attach(Bio6)
> head(Bio6)
> par(family="serif", font=11)
> Bio6$Sps<- factor(Bio6$Sps, levels = c("FFA1", "FFA2","FFA3"))
> Bio6$Gp<- factor(Bio6$Gp, levels = c("N-FFA1",
> "FU1","FA1","N-FFA2","FU2","FA2","N-FFA3","FU3","FA3"))
> bargraph.CI(Sps, O.D, group = Gp, data = Bio6,ylab = "Relative expression
> levels", cex.lab = 1.5, y.leg = 6,cex.leg = 0.82,cex=1.5, axisnames=TRUE,
> col = c("red","blue","grey"),space=c(0, 0.5), ylim=c(0,7),cex.names =
> 1.0,density = c(30,30,30), legend = TRUE, main="PLIN1")
> detach(Bio6)
>
>   O.D     Gp  Sps
> 1  1.000000 N-FFA1 FFA1
> 2  2.996432    FU1 FFA1
> 3  3.223413    FU1 FFA1
> 4  3.524465    FU1 FFA1
> 5  1.311971    FA1 FFA1
> 6  6.755860    FA1 FFA1
> 7  1.566000    FA1 FFA1
> 8  1.000000 N-FFA2 FFA2
> 9  2.741612    FU2 FFA2
> 10 2.800644    FU2 FFA2
> 11 3.569509    FU2 FFA2
> 12 4.141500    FA2 FFA2
> 13 7.049476    FA2 FFA2
> 14 4.694674    FA2 FFA2
> 15 1.000000 N-FFA3 FFA3
> 16 4.163601    FU3 FFA3
> 17 3.903986    FU3 FFA3
> 18 4.730000    FU3 FFA3
> 19 0.000000    FA3 FFA3
> 20 0.000000    FA3 FFA3
> 21 0.000000    FA3 FFA3
>
Hi Roopa,
bargraph.CI does something with the "space" argument that I can't quite 
work out. I can get a reasonable plot like this:

Bmeans<-matrix(by(Bio6$O.D,Bio6$Gp],FUN=mean),ncol=3)
barpos<-barplot(Bmeans,beside=TRUE,
  ylim=c(0,7),col=c("red","blue","grey"),space=c(0.1,1),main="PLIN1")
legend(8.5,7.1,
  c("N-FFA1","FU1","FA1","N-FFA2","FU2","FA2","N-FFA3","FU3","FA3"),
  fill=c("red","blue","grey"),bty="n")
library(plotrix)
Bse<-matrix(by(Bio6$O.D,Bio6$Gp,FUN=std.error),ncol=3)
dispersion(barpos,Bmeans,Bse,display.na=FALSE)

Jim