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rpdfggplot2gghighlight

Loop to save same plot with different highlights using ggplot2

I would like to use ggplot to create multiple density plots that have the same data but that show a specific line highlighted. The table I have is extremely big but has the following columns:

Marker  Sample  value
X1      4_HVxLF 0.5
X2      4_HVxLF 0.1
...

Here is what I get by plotting all the lines together.

ggplot(Dta, aes(x=value, group=Sample, color = Sample)) +
  geom_density()+
  xlab("value")+
  ylab("Density")+
  theme_classic()

It is not easy to interpret. Then, My aim is to get something like this: desired plot. The code used is:

ggplot(Dta, aes(x=value, group=Sample, color = Sample)) +
  geom_density()+
  xlab("value")+
  ylab("Density")+
  theme_classic()+
  gghighlight(SampleName == "25_HVxLF",
              unhighlighted_params = list(colour = "grey90"))

So I tried building a loop to get a PDF with 4 plots like the second one per page and for all my samples (105 of them). I cannot used facet_wrap because there are too many of them. Here is what I tried:

Samples <- unique(Dta$Sample)    
pdf('Allplots.pdf', width = 8, height = 11)
    par(mfrow=c(4,2))
    for (i in Samples){
      ggplot(Dta, aes(x=value, group=Sample, 
                             color = Sample)) +
        geom_density()+
        xlab("value")+
        ylab("Density")+
        theme_classic()+
        gghighlight(Sample == Samples[i],
          unhighlighted_params = list(colour = "grey90"))
    }
dev.off()

But the PDF that comes out is 4kb and I cannot open it. It says there are no pages. I am not used to work with loops so this is my first attempt ... I don't know what I did wrong (maybe many things), could someone help me figure out ?

Thank you in advance for your kind help !

Diana

Solution

  • Using patchwork and lapply to loop over your samples one approach to achieve your desired result may look like so:

    1. Use a first loop to create your plots and store them in a list
    2. Use a second loop to glue the plots together in grids of 2 rows and 2 columns using patchwork::wrap_plots

    Making use of some fake random example data:

    library(ggplot2)
library(gghighlight)
library(patchwork)

plot_fun <- function(highlight) {
  ggplot(Dta, aes(x=value, group=Sample, 
                color = Sample)) +
  geom_density()+
  xlab("value")+
  ylab("Density")+
  theme_classic()+
  gghighlight(Sample == highlight,
              unhighlighted_params = list(colour = "grey90"))
}

Samples <- unique(Dta$Sample)

# Make plots
p <- lapply(Samples, plot_fun)

nrow <- 2
ncol <- 2

# Page counter
idx_page <- rep(seq(ceiling(length(p) / nrow / ncol)), each = nrow * ncol, length.out = length(p))

# Export plots as grids of 2 x 2
pdf('Allplots.pdf', width = 8, height = 11)
lapply(unique(idx_page), function(x) {
  wrap_plots(p[idx_page == x], ncol = ncol, nrow = nrow)
})
#> [[1]]
#> 
#> [[2]]
#> 
#> [[3]]
#> 
#> [[4]]
#> 
#> [[5]]
dev.off()
#> quartz_off_screen 
#>                 2

    DATA

    # Random example data
set.seed(123)
n <- 20
Dta <- data.frame(
  Sample = rep(LETTERS[seq(n)], each = 100),
  value = rnorm(100 * n)
)