qplotMS1data: Quick plot for MS data

In RaMS: R Access to Mass-Spec Data

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
)

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.

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.

Examples

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:
## Not run: 
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)])

## End(Not run)

RaMS documentation built on Oct. 9, 2024, 9:06 a.m.