plotSpectra: Plot and Compare Spectra

In wesleyburr/subMaldi: Organization and Processing of MALDI-MS Datasets

Description

Plot single or multiple spectra. For multiple spectra, a grid layout can be called using 'nrows'.

Usage

plotSpectra(
  dat,
  mass_dat,
  spectra_cols,
  palette = NULL,
  colours = (grDevices::colorRampPalette(c("#cc6600",
    "#33ccff")))(length(spectra_cols)),
  span = 5,
  thresh = 0.1,
  lbls = FALSE,
  lbl.fmt = "%3.4f",
  min_mz = min(dat[[mass_dat]]),
  max_mz = max(dat[[mass_dat]]),
  min_I = 0,
  max_I = max(dat[spectra_cols]),
  x_ticks = 100,
  nrows = ceiling(length(spectra_cols)/2),
  intensity_scale = "free_y"
)

Arguments

dat	The name of the spectral data frame, containing the m/z data in the first column.
mass_dat	A character string; the name of the column in dat containing the m/z data.
spectra_cols	A character string; the name(s) of the column(s) in dat containing the intensity data for the spectra-of-interest.
palette	A character element; the RColorBrewer palette to use. See below for available palettes.
colours	A character string indicating the desired colour(s)
span	Single numeric value; the span of peak maxima in between each label. Default = 5 (ignores two peak maxima on either side of each label).
thresh	Single numeric value (0-100); the threshold of peak intensities which should be labeled.
lbls	Logical. If lbls = TRUE, labels indicating the m/z value of each peak maxima within the indicated span will be included in the output plot. If lbls = FALSE, labels are not shown.
lbl.fmt	Character string in the format "%a.bf", where a is the number of figures displayed to the left of decimal places in labels, and b is the number of figures displayed to the right of decimal places in labels. Default = "%3.4f".
min_mz	Single numeric value; minimum m/z value of the observed range.
max_mz	Single numeric value; upper end of m/z range observed in spectra.
min_I	Single numeric value; minimum intensity value of the observed range.
max_I	Single numeric value; upper end of the intensity range observed in spectra.
x_ticks	Single numeric value; the number of ticks on the x-axis.
nrows	Single integer value; the number of rows in plot arrangement.
intensity_scale	A character string; the method that should be used for determining the y-axis scales for each spectrum. If method = "free_y", each spectrum will be plotted with its own intensity scale. If method = "fixed", each spectrum will be plotted with the y-axis of the most intense spectrum in the set.

Value

Returns a line plot of the input spectra.

RColorBrewer Palettes

• "Accent"

• "Dark2"

• "Paired"

• "Pastel1"

• "Pastel2"

• "Set1"

• "Set2" (default)

• "Set3"

Author(s)

Kristen Yeh <[e-mail]> Wesley Burr <[e-mail]> Sophie Castel <[e-mail]>

References

https://github.com/wesleyburr/subMaldi

Examples

## Plotting using the sample dataset "Master.rda"
data("Master")
plotSpectra(dat = Master, mass_dat = "full_mz",
            spectra_cols = c("Blank1", "Blank2"),
            intensity_scale = "free_y", lbls = TRUE, nrows = 2, x_ticks = 10)

wesleyburr/subMaldi documentation built on Oct. 1, 2021, 7:07 a.m.