Improvement suggestion: highlightChromPeaks by filling the area of the detected peaks

[etrh]

Would it be possible to add a new functionality to highlightChromPeaks that would fill the area of the detected peaks instead of drawing rectangles around them? It is sometimes difficult to understand what is exactly being picked as a peak by looking at the rectangles.

An example of the feature I am requesting is implemented in Agilent MassHunter:

[jorainer]

Yup, that would look definintely better - I'll think of a way to do that. If you have already an idea in mind you are also welcome to implement that and create a pull request.

[stanstrup]

If you are using ggplot2 this is probably what you need to implement that:
http://www.sthda.com/english/wiki/ggplot2-area-plot-quick-start-guide-r-software-and-data-visualization#coloring-under-density-curve-using-geom_area

To avoid the warnings that gives (because they put zero height) I assume you can create an appropriate matrix for each segment instead that only contains the segment.

Can intervals overlap? In that case alpha=0.5 or something like that.

[stanstrup]

I was curios so I wrote something. Here it is in case it is helpful. I apologize for the tidyverse syntax. I can't really think in standard R terms anymore...

library(ggplot2)
library(dplyr)
library(purrr)
library(tidyr)


df <- data.frame(
  sex=factor(rep(c("F", "M"), each=200)),
  weight=round(c(rnorm(200, mean=55, sd=5),
                 rnorm(200, mean=65, sd=5)))
  )



dat <- with(density(df$weight), data.frame(x, y)) %>% 
        filter(x>30 & x< 80)



intervals <- data.frame(start = c(40,65, 47), end = c(50,70, 60)) %>% 
             mutate(interval = as.factor(1:nrow(.))) %>% 
             mutate(interval_dat = map2(start,end, ~dat %>% filter(x>..1 & x<..2))) %>% 
             select(interval,interval_dat) %>% 
             unnest



ggplot(data = dat, mapping = aes(x = x, y = y)) +
    geom_line() + 
    geom_area(data=intervals, aes(fill = interval), position = "identity", alpha=0.5)

[jorainer]

@stanstrup for your input! For basic R plotting it can be done with polygon. Only thing is that the actual chromatogram data has to be read also within highlightChromPeaks.

[jorainer]

OK, implementation was easier than expected. @etrh if you want to use it you'll have to install the latest version from github. There is now the possibility to select type = "polygon" in highlightChromPeaks. Peaks will be filled with the color defined with argument col and drawn with border (set to NA to not draw any borders).

[etrh]

Thanks for being so quick with this! Much appreciated. It works very well and I will continue using it and report any bugs that might arise later on. Thanks again. A very useful feature.

[jorainer]

So I'm closing this issue for now. Feel free to re-open if you encounter problems.