R: ggplot2 and loop with data.table

Question

I have to make 4 plots which differ only for y and ylab. I start from a data.table dt which is

set.seed(123)
dt <- data.table(a = rnorm(20),
                 b = rnorm(20), 
                 c = rnorm(20), 
                 d = rnorm(20), 
                 e = rnorm(20))

Every single plot should be a scatterplot with row numbers as x vs y values. Additionally, I want to plot some hline at median(y) + h*mad(y) where h = c(0, -2, 2, -3, 3)

This plot should be repeated for columns a, c, d and e of dt.

I came up with this bit of code

# Defining y labels #
ylabels <- c(bquote(phantom(.)^100*A~"/"*phantom(.)^200*A),
             bquote(phantom(.)^101*C~"/"*phantom(.)^201*B),
             bquote(phantom(.)^102*D~"/"*phantom(.)^202*D),
             bquote(phantom(.)^103*E~"/"*phantom(.)^202*E))

# Selecting columns of dt    
ydata <- names(dt)[c(1, 3, 4, 5)]


h <- c(0, -2, 2, -3, 3)
hcol <- c("#009E73", "#E69F00", "#E69F00", "red", "red")

# The for cycle should create the 4 plots and assign them to a list 
plots <- list()
for (i in seq_along(ydata)) {

    p1 <- ggplot(dt, aes_string(x = seq(1, dt[, .N]), y = ydata[i])) +
                     geom_point() +
                     geom_hline(aes_string(yintercept = median(ydata[i]) + 
                                       h * mad(ydata[i])), color = hcol) +
                     xlab("Replicate") + 
                     ylab(ylabels[i]) +
                     scale_x_continuous(breaks = seq(1, dt[,.N])))

     plots[[i]] <- p1  # add each plot into plot list
     }

Then plots will be fed to the multiplot function from Cookbook for R.

However my loop doesn't work properly because it fails to calculate the median and mad values. Do you have any suggestions to make the code work?

Ndr · Accepted Answer · 2017-03-08 17:45:42Z

# data.table with the median +- h* mad values
hline.values <- dt[, lapply(.SD, function(x) median(x) + h * mad(x)),
                   .SDcols = ydata]

# new empty list
plots <- list()

for (i in seq_along(ydata)) {

       p1 <- ggplot(dt, aes_string(x = seq(1, dt[, .N]), y = ydata[i])) +
             geom_point() +
             geom_hline(data = hline.values, 
                        aes_string(yintercept = ydata[i])) +
             # Axis labels and theme
             xlab("Replicate") +
             ylab(ylabels[[i]]) +
             scale_x_continuous(breaks = seq(1, dt[, .N]))

        plots[[i]] <- p1
}

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