6

I made ggplot which presents population numbers of one species. This script works well. So I made for-loop to chain produce this plot for 25 species, but it doesn't works.

Here's an example for one species :

A <- data.frame(sp="A",x=c(rep(0.1,3),rep(2,3),rep(4.5:8.5,4),6.5), width=c(rep(NA,3), rep(4,3), rep(1,20),5),y=c(rep(1:3,2), rep(1:4, each=5),5),col=c(rep("white",21), rep("grey80",6)), name1=c("C.I. (%)","C.N. (%)", rep("",25)), name1i=c(rep("",2), "Total",rep("",24)), nb1=c(rep(NA,7),1.33,0.53,0.52,0.42,NA,27.12,10.90,10.55,8.56,rep(NA,11)),nb2=c(rep(NA,16),24754,13558,5449,5273,4281,rep(NA,6)),nb3=c(rep(NA,6),2.43,rep(NA,4),49.51, rep(NA,15)), name2=c(rep("",21),"J","F","M","A","M","Month"))

library(ggplot2)
library(gridExtra)
  table <- A
  windows()
  ggplot(table, aes(x=x, y=y, width=width, fill=col))+
    geom_tile(colour="black")+
    scale_fill_manual(values = c("white"="white", "grey80"="grey80"),    
                      breaks = levels(table$col), na.value = "white")+
    geom_text(aes(label=name1), size=6, hjust=0)+
    geom_text(aes(label=name1i), size=6, hjust=0, fontface=3)+
    geom_text(aes(label=nb1), size=6)+
    geom_text(aes(label=nb2), size=6, fontface=3)+
    geom_text(aes(label=nb3), size=6, fontface="bold")+
    geom_text(aes(label=name2), size=6, fontface="bold")+
    coord_cartesian(xlim=c(0,9), ylim=c(0.5,5.5))+
    labs(x = "",y = "") +                   
    scale_x_discrete(expand = c(0, 0)) +   
    scale_y_discrete(expand = c(0, 0))+     
    theme(axis.ticks = element_blank(),     
          axis.text = element_blank(),      
          legend.position = "none",        
          panel.background = element_rect(fill='white', colour='white'),   
          plot.margin = unit(c(0.5,0.5,-1,-1), "lines"))

enter image description here

And for two species with for-loop :

A <- data.frame(sp="A",x=c(rep(0.1,3),rep(2,3),rep(4.5:8.5,4),6.5), width=c(rep(NA,3), rep(4,3), rep(1,20),5),y=c(rep(1:3,2), rep(1:4, each=5),5),col=c(rep("white",21), rep("grey80",6)), name1=c("C.I. (%)","C.N. (%)", rep("",25)), name1i=c(rep("",2), "Total",rep("",24)), nb1=c(rep(NA,7),1.33,0.53,0.52,0.42,NA,27.12,10.90,10.55,8.56,rep(NA,11)),nb2=c(rep(NA,16),24754,13558,5449,5273,4281,rep(NA,6)),nb3=c(rep(NA,6),2.43,rep(NA,4),49.51, rep(NA,15)), name2=c(rep("",21),"J","F","M","A","M","Month"))
B <- data.frame(sp="B",x=c(rep(0.1,3),rep(2,3),rep(4.5:8.5,4),6.5), width=c(rep(NA,3), rep(4,3), rep(1,20),5),y=c(rep(1:3,2), rep(1:4, each=5),5),col=c(rep("white",21), rep("grey80",6)), name1=c("C.I. (%)","C.N. (%)", rep("",25)), name1i=c(rep("",2), "Total",rep("",24)), nb1=c(rep(NA,6),4.5,6.74,3.43,3.56,NA,19.89,29.82,15.18,15.75,rep(NA,12)),nb2=c(rep(NA,16),3282,4920,2504,2599,5328,rep(NA,6)),nb3=c(rep(NA,10),7.30,rep(NA,4),32.29, rep(NA,11)), name2=c(rep("",21),"J","F","M","A","M","Month"))
data <- rbind(A,B)
sp <- c("A","B")

library(ggplot2)
library(gridExtra)
for(i in sp){
  table <- data[data$sp==i,]
  windows()
  ggplot(table, aes(x=x, y=y, width=width, fill=col))+
    geom_tile(colour="black")+
    scale_fill_manual(values = c("white"="white", "grey80"="grey80"),    
                      breaks = levels(table$col), na.value = "white")+
    geom_text(aes(label=name1), size=6, hjust=0)+
    geom_text(aes(label=name1i), size=6, hjust=0, fontface=3)+
    geom_text(aes(label=nb1), size=6)+
    geom_text(aes(label=nb2), size=6, fontface=3)+
    geom_text(aes(label=nb3), size=6, fontface="bold")+
    geom_text(aes(label=name2), size=6, fontface="bold")+
    coord_cartesian(xlim=c(0,9), ylim=c(0.5,5.5))+
    labs(x = "",y = "") +                   
    scale_x_discrete(expand = c(0, 0)) +   
    scale_y_discrete(expand = c(0, 0))+    
    theme(axis.ticks = element_blank(),    
          axis.text = element_blank(),     
          legend.position = "none",         
          panel.background = element_rect(fill='white', colour='white'),   
          plot.margin = unit(c(0.5,0.5,-1,-1), "lines"))  
}

Plot is empty without error message, so I do not understand where is my error. Is it just a ggplot problem? In fact I don't think so, because other ggplot works well with for-loop... Do you have any idea? Thanks for your help!

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3
  • pl = plyr::dlply(data, "sp", "%+%", e1=last_plot()); do.call(grid.arrange, pl) Commented Jan 21, 2014 at 17:29
  • @Ma. I've deleted my answer since it didn't work. Commented Jan 21, 2014 at 21:06
  • Thank you baptiste and amzu for your interest in my problem. I think simplest solution is @jlhoward answer. Commented Jan 22, 2014 at 9:07

3 Answers 3

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13

The problem is the for loop. You need to use print in a loop.

for (i in sp) {
  table <- data[data$sp=="A",]
  windows()
  ggp <- ggplot(...) + ...
  print(ggp)
}

Consider this simple example:

library(ggplot2)
df=data.frame(x=1:10,y=rnorm(10))                       # sample data
ggplot(df)+geom_point(aes(x,y))                         # render ggplot
for (i in 1:2) ggplot(df)+geom_point(aes(x,y))          # nothing
for (i in 1:2) print(ggplot(df) + geom_point(aes(x,y))) # renders

Also, as @user229552 says, you are using the same table both times.

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Comments

2

For starters, it looks like you're always picking the "A" subset. The beginning of the for loop should look like:

for(i in sp){
 table <- data[data$sp==i,]
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0

using print() is required with qplot() as well in for loop

e.g. I had the following format of code but only blank image files were created when using qplot()

for(loop1 in rangestart:rangeend)  
{  
   ..........  
   ..........  
   png(Imagefile,width=1366,height=768)  
   qplot(.....)  
   dev.off()  
}

Replacing qplot(.....) with print(qplot(.....)) solved the problem

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