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Default plot methods for optical data with ggplot2

Source: R/plot.R
plot.Rd

Used to make a nice plot of one or multiple excitation emission matrices (EEMs) or absorbance spectra using ggplot2.

Usage

# S3 method for class 'eem'
plot(
  x,
  nbin = 8,
  equal_scale = FALSE,
  pal = NULL,
  title = "none",
  remove_lower = FALSE,
  annotate = FALSE,
  index_method = "eemanalyzeR",
  ...
)

# S3 method for class 'eemlist'
plot(
  x,
  nbin = 8,
  equal_scale = FALSE,
  pal = NULL,
  remove_lower = FALSE,
  title = "none",
  annotate = FALSE,
  index_method = "eemanalyzeR",
  ...
)

# S3 method for class 'abs'
plot(x, pal = NULL, ...)

# S3 method for class 'abslist'
plot(x, pal = NULL, ...)

Arguments

x

An eemlist, eem, abslist, or abs object.

nbin

Number of bins used in the contour plot.

equal_scale

Logical. If TRUE, sets the scale the same for all plots in an eemlist.

pal

Color palette for the fill scale. Defaults to pals::parula(). If fewer colors are provided than required, grDevices::colorRampPalette() is used to fill in colors.

title

Either "none", "meta_name", or "sample" which indicates what to use for the plot title.

remove_lower

Logical. If TRUE, sets values below the first-order Rayleigh line to NA, which can reduce artifacts affecting the color scale.

annotate

Logical. If TRUE, displays index regions on EEM plots.

index_method

Either "eemanalyzeR", "eemR", "usgs".

...

Additional arguments passed to plot.

Value

  • If x is an eem, abs, or abslist: a single ggplot2 object.

  • If x is an eemlist: a list of ggplot2 objects.

Details

Single EEM plots return a ggplot2 object, compatible with other ggplot2 modifications. Multiple EEMs return a list of ggplot2 objects, which can be individually modified. See examples for usage.

Note

Slow plotting may be due to your default graphics device. See https://forum.posit.co/t/graphics-not-working-in-rstudio/149111 for guidance.

See also

ggplot2::ggplot()

Examples

eems <- example_processed_eems
abs <- example_processed_abs

# plot just one eem/abs
plot(eems[[3]])

plot(abs[[3]])


# plot all in an eemlist or abslist
eem_plots <- plot(eems)
abs_plots <- plot(abs)

# change color scale
plot(eems, pal = c("darkblue", "lightblue"))

# make color bar consistent across all plots
plot(eems[2:3], equal_scale = TRUE)

# customize using ggplot2 commands
plot(eems[[2]]) + ggplot2::labs(title = "Test EEM")

eem_plots[[3]] + ggplot2::labs(title = "Test EEM")


# modify then arrange together
eem_plots[[3]] <- eem_plots[[3]] + ggplot2::labs(title = "Test EEM")
print(ggpubr::ggarrange(plotlist = eem_plots))


# remove lower area below rayleigh line
plots <- plot(eems[[3]], remove_lower = TRUE)