ggplot subsetting in loop

Question

here is a problem I have with ggplot+ lapply+ subsetting problem

here a reproducible exemple

stages=as.vector(c("1","2","3","1","1","1","1","1","1","2","2","2","2","2","3","3","3","3","3","3","3","3","3","3","3","1","1"))
x13=c(0.9, 0, 0, 0.692, 0,0,0,0,0,0,0,0,0,0.53, 0.5,0,2,3,55,49,64,9,4,1,0,54,0)
y13=c(0.9, 0, 0, 0.692, 0,0,0,0,0,0,0,0,0.53,0.9, 0, 0, 0.692, 0,0,0,0,0,0,0,0,0,0.53)
countmatrix=cbind(x13,stages,y13)
countmatrix=as.data.frame(countmatrix)
p2=ggplot(data=countmatrix, aes(stages, fill = x13))+
  geom_bar(position="stack",  fill="gray34")+
  geom_bar(data=subset(countmatrix, x13!=0),  aes(fill=stages ))
p2 ````

once I put it in function to replicate over many variable it seems to not work (the subsetting part at least seems to not work. here is the code I used.

barplotseries <- function(x){
  y=as.name(x)
  ggplot(data=countmatrix, aes(stages, fill = y))+
    geom_bar(position="stack",  fill="gray34")+
    geom_bar(data=subset(countmatrix,y!=0),  aes(fill=stages ))
}
x=c("x13","y13")
p2=lapply(x, barplotseries)
do.call("grid.arrange", c(p2, ncol=2))

all want is to be able to make the same plot above on as many variables as possible.

please let me know you suggestions (should I use For?) I don't know how to use it.

thanks

Save the plot inside your function using a variable so you can access it outside the function. — deepseefan
– deepseefan, Commented Oct 29, 2019 at 14:59
Also, reproducible example as is does not render such a plot. Please be sure to re-run posted code in an empty R environment (i.e., no previous globalenv objects) to make sure all compiles and renders accordingly. — Parfait
– Parfait, Commented Oct 29, 2019 at 15:09
Sorry I forgot to copy the first line. the vector stages is in now. it's reproducible now. — YBKL
– YBKL, Commented Oct 30, 2019 at 15:08

StupidWolf · Accepted Answer · 2019-11-05 22:56:32Z

1

Along the lines to what @Parfait pointed out, not a good idea to call globalenv objects.

Your original function doesn't work because 1. it takes in a string and you pass it into aes in ggplot2, 2. when you subset on countmatrix, you are passing the string in again..

Make a few edits and below should work:

#keep the data.frame as factors and numeric
stages=as.vector(c("1","2","3","1","1","1","1","1","1","2","2","2","2","2","3","3","3","3","3","3","3","3","3","3","3","1","1"))
x13=c(0.9, 0, 0, 0.692, 0,0,0,0,0,0,0,0,0,0.53, 0.5,0,2,3,55,49,64,9,4,1,0,54,0)
y13=c(0.9, 0, 0, 0.692, 0,0,0,0,0,0,0,0,0.53,0.9, 0, 0, 0.692, 0,0,0,0,0,0,0,0,0,0.53)
countmatrix=data.frame(x13,stages,y13)

your edited function

barplotseries <- function(y,DATA){
  DATA_subset = subset(DATA,DATA[,y]>0)      
  ggplot(data=DATA, aes_string(x="stages", fill = y))+
    geom_bar(position="stack",  fill="gray34")+
    geom_bar(data=DATA_subset,  aes(fill=stages ))
}

combining the plots

x=c("x13","y13")
p2=lapply(x,function(i)barplotseries(i,countmatrix))
do.call("grid.arrange", c(p2, ncol=2))

You can also do other types of subsetting, like the y column greater than some cutoff:

barplotseries <- function(y,DATA){
  DATA_subset = subset(DATA,DATA[,y]>mean(DATA[,y])-1.96*sd(DATA[,y]))
  ggplot(data=DATA, aes_string(x="stages", fill = y))+
    geom_bar(position="stack",  fill="gray34")+
    geom_bar(data=DATA_subset,  aes(fill=stages ))
}

edited Nov 5, 2019 at 22:56

answered Oct 30, 2019 at 22:18

StupidWolf

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13 Comments

YBKL Over a year ago

Hey Man! thank you so Much. it worked flawlessly!!! thanks a lot!

StupidWolf Over a year ago

what is your subsetting rule now? I hope it is not too complex =p

YBKL Over a year ago

I want to remove the to bottom 5% of the values (through a Z scoore eliminatation) data=subset(DATA,DATA[,y]>(mean(y))-1.96*sd(y)), but it doesn't work

YBKL Over a year ago

if I put a value like data=subset(DATA,DATA[,y]> 0 or 1 or 2. it works, but it I put a formula it doesn't (like (mean(y))-1.96*sd(y)))

StupidWolf Over a year ago

you have to call DATA[,y] again, because y here is a character.. so do something like data=subset(DATA,DATA[,y]>(mean(DATA[,y]))-1.96*sd(DATA[,y]))

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