Question

I’m trying to use a for loop and an if statement in my R code, as below.

It produces a density plot, and I am then trying to add a vertical line to the density which is coloured by species. 

When I print(organism) within the for loop it prints the Species column 4 times, why does it not print it out once? So therefore is it cycling 4 times through my data?

The code manages to add some red lines to the density plot, but why is it not adding the remaining coloured lines for the other species?

dat <- structure(list(pdb = structure(1:13, .Label = c("1akk.pdb", "1fi7.pdb", 
"1fi9.pdb", "1giw.pdb", "1hrc.pdb", "1i5t.pdb", "1j3s0.10.pdb", 
"1j3s0.11.pdb", "1j3s0.12.pdb", "1j3s0.13.pdb", "1j3s0.14.pdb", 
"2aiu.pdb", "2b4z.pdb"), class = "factor"), PA = c(1128, 1143, 
1119, 1130, 1055, 1112, 1120, 1121, 1135, 1102, 1121, 1037, 1179
), EHSS = c(1424, 1439, 1404, 1423, 1318, 1403, 1412, 1415, 1432, 
1391, 1413, 1299, 1441), Species = structure(c(2L, 2L, 2L, 2L, 
2L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 1L), .Label = c("BOSTAURUS", 
"EQUUSCABALLUS", "HOMOSAPIENS", "MUSMUSCULUS"), class = "factor")), .Names = c("pdb", 
"PA", "EHSS", "Species"), class = "data.frame", row.names = c(NA, 
-13L))

den.PA <- density(dat$PA)
plot(den.PA)

for (i in 1:length(dat)){
    lineat = dat$PA[i]
    organism = dat$Species[i]
    lineheight <- den.PA$y[which.min(abs(den.PA$x - lineat))]
    print (organism)
    if (organism == 'EQUUSCABALLUS'){
        col = 'red'
    }
    if (organism == 'HOMOSAPIENS'){
        col = 'blue'
    }
    if (organism == 'MUSMUSCULUS'){
        col = 'green'
    }
    if (organism == 'BOSTAURUS'){
        col = 'purple'
    }
    lines(c(lineat, lineat), c(0, lineheight), col = col)
}

Answer 1

taking your dat from dput(), you can change your code to iterate over the rows, and first convert the the PA to class character before extracting the element. That way you’ll get 13 lines:

    den.PA <- density(dat$PA)
    plot(den.PA)

    for (i in 1:nrow(dat)){
        lineat <- dat$PA[i]
        organism <- as.character(dat$Species)[i]
        lineheight <- den.PA$y[which.min(abs(den.PA$x - lineat))]
        print (organism)
        if (organism == 'EQUUSCABALLUS'){
            col <- 'red'
        }
        if (organism == 'HOMOSAPIENS'){
            col <- 'blue'
        }
        if (organism == 'MUSMUSCULUS'){
            col <- 'green'
        }
        if (organism == 'BOSTAURUS'){
            col <- 'purple'
        }
        segments(lineat,0,lineat,lineheight,col=col)
    }

also, I changed lines() to segments(), since you just have 2 points. That doesn’t make much difference however. I also changed declarations using = to <-, which hurts the eyes of most R users less.