Plotting upper quanitles only from dataframe containg all values

Question

I have a large dataframe,df, which contains a list of nonunique identifiers (Cell.ID) and information within that identifier. It looks something like this:

    Cell.ID Volume
1   025001G 2.08
2   025001G 0.30
3   025001G 0.99
4   025001G 0.60
5   025001G 0.43
6   025001G 0.24
7   025001G 0.59
8   025001R 1.74
9   025001R 1.09
10  025001R 0.58
11  025001R 0.75
12  025001R 0.62
13  025002G 8.59
14  025002G 1.26
15  025002R 6.31
16  025002R 0.56
17  025003G 1.95
18  025003G 2.18
19  025003G 0.21

What I would like to do is make a plot where the Y axis corresponds to Volume and the X coordinate corresponds to number of instances of a particular Cell.ID. This part was straight forward, but I would like the Y coordinate for each object to either be a box spanning the upper two quantiles or a point representing the second highest quantile. Using tapply(df$Volume,quantile) , and table(df$Cell.ID) I was able to create a data frame that looks like the one below, which contains the requisite information to make said plot. Freq contains information on how many times a particular Cell.ID (row name) has shown up and Quantile contains the information on the distribution of volumes for objects in that Cell.ID.

 row.names       quantile                        Var1     Freq
1   010001G c(0.27, 0.27, 0.325, 0.6125, 1.31)    010001G   4
2   010001R c(0.22, 0.365, 0.51, 0.655, 0.8)     010001R    2
3   010002G c(0.67, 0.8025, 0.935, 1.0675, 1.2)  010002G    2
4   010002R c(0.25, 0.41, 0.57, 0.73, 0.89)      010002R    2
5   010003G c(0.22, 0.295, 0.345, 0.3725, 0.38)  010003G    4
6   010003R c(0.22, 0.2675, 0.315, 0.3625, 0.41) 010003R    2
7   010004G c(0.35, 0.41, 0.625, 1.165, 2.2)     010004G    4
8   010004R c(0.2, 0.4075, 0.615, 0.8225, 1.03)  010004R    2
9   010005G c(3.95, 3.95, 3.95, 3.95, 3.95)      010005G    1
10  010005R c(0.47, 0.775, 1.08, 2.53, 3.98)     010005R    3
11  010006G c(0.25, 0.98, 1.71, 2.98, 4.25)      010006G    3

However I'm stuck on how to select only certain quantiles in each row to plot from the quantile column. I've tried a few things but get errors such as this:

Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' is a list, but does not have components 'x' and 'y 

Answer 1

If I understand your question correctly you don't need all quantiles, just one or two of them. So you can try something like that:

Q75 <- tapply(df$Volume, df$Cell.ID, quantile, probs = 0.75)
freq <- table(df$Cell.ID)
plot(x = as.vector(freq), y = Q75, 
     xlab = "Frequency", ylab = "75th Quantile")

Or for the 75th and 95th quantiles:

Q7595 <- do.call(rbind.data.frame, 
                 tapply(df$Volume, df$Cell.ID, quantile, 
                        probs = c(0.75, 0.95), simplify = TRUE))
## Empty plot
matplot(x = as.vector(freq), y = Q7595, type = "n", 
        xlab = "Frequency", ylab = "75th and 95th Quantiles")
## Boxes 
rect(xleft = as.vector(freq) - 0.25, xright = as.vector(freq) + 0.25, 
     ytop = Q7595[,1], ybottom = Q7595[,2])

The result looks like that:

Of course it needs some aesthetic changes, but I hope it helps, alex