RaMS (version 1.4.3)

qplotMS1data: Quick plot for MS data

Description

Syntactic sugar for a common chromatogram plot. Will use `ggplot2` if available but has a base plot implementation for use even in ultra lightweight situations. Accepts the default MS1 output from `grabMSdata` of a data.table (or base data.frame) with columns for rt (retention time) and int (intensity) as well as filename. Creates a plot of intensity vs retention time with one trace per file. A few additional `ggplot2` arguments are also made available for easy coloring or facetting by providing the name of the associated column to the `color_col` and `facet_col` arguments, respectively.

Usage

qplotMS1data(
  MS1_df,
  color_col = NULL,
  facet_col = NULL,
  facet_args = list(ncol = 1),
  force_base = FALSE
)

Value

If `ggplot2` is installed, a `ggplot` object that can be further modified via additional + commands. Otherwise, NULL and the plot appears via base graphics at the active device.

Arguments

MS1_df

A data.table with at least three columns named rt, int, and filename

color_col

The name of the column to color by. Must be quoted.

facet_col

The name of the column to facet by. Must be quoted.

facet_args

Since the call to facet_wrap is within the function, you can provide additional facet customization arguments here as a list. Although if you're starting to fiddle with facets you'll probably be better served by the proper `ggplot` call.

force_base

Boolean option to force base R graphics instead of `ggplot` even if the `ggplot2` package is installed.

Examples

data.table::setDTthreads(2)
test_df <- expand.grid(rt=rep(1:100, length.out=1000))
test_df$int <- rep(dnorm(seq(-10, 10, length.out=100)), 10)*10+runif(1000)
test_df$filename <- rep(LETTERS[1:10], each=100)
qplotMS1data(test_df)

test_df$startime <- rep(gl(2, 5, labels = c("Morn", "Eve")), each=100)
qplotMS1data(test_df, color_col="startime", facet_col="startime")
qplotMS1data(test_df, color_col="startime", facet_col="startime",
            facet_args=list(ncol=2, scales="free"))

# Using data from the `grabMSdata` function:
if (FALSE) {
sample_dir <- system.file("extdata", package = "RaMS")
sample_files <- list.files(sample_dir, full.names=TRUE)
msdata <- grabMSdata(sample_files[c(3, 5, 6)], grab_what="MS1")
qplotMS1data(msdata$MS1[mz%between%pmppm(118.0865)])
}