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Create a Custom Plot for Spectral Data

Source: R/spec_smartplot.R
spec_smartplot.Rd

This function generates a customizable plot for spectral data, allowing for the selection of plot type (absorbance or transmittance), x-axis direction, plot geometry (points or lines), and color palette.

Usage

spec_smartplot(
  .data,
  wn_col = NULL,
  xdir = c("reverse", "standard"),
  geom = c("point", "line"),
  xmin = NULL,
  xmax = NULL,
  alpha = 0.8,
  type = c("absorbance", "transmittance"),
  palette = c("viridis", "plasma", "magma", "cividis", "turbo", "Set1", "Set2", "Dark2",
    "Paired", "custom"),
  custom_colors = NULL
)

Arguments

.data

A `data.frame` or `tibble` containing spectral data.

wn_col

A character string specifying the column name for the wavelength or wavenumber data. This parameter is required.

xdir

A character string specifying the direction of the x-axis. Choices are `"reverse"` (typically used for wavenumber) or `"standard"`.

geom

A character string specifying the geometry of the plot. Choices are `"point"` for a scatter plot or `"line"` for a line plot.

xmin

A numeric value specifying the minimum x-axis value. If not provided, the minimum value from `wn_col` will be used.

xmax

A numeric value specifying the maximum x-axis value. If not provided, the maximum value from `wn_col` will be used.

alpha

A numeric value (0–1) specifying the transparency of plotted points or lines. Default is `0.8`.

type

A character string specifying the y-axis label. Either `"absorbance"` (default) or `"transmittance"`.

palette

A character string specifying the color palette to use. Built-in options:

`"viridis"`

Perceptually uniform, colorblind-friendly (default).

`"plasma"`

High-contrast warm-to-cool gradient.

`"magma"`

Dark-to-light, suitable for dark backgrounds.

`"cividis"`

Optimized for color vision deficiency.

`"turbo"`

Full-spectrum rainbow with high contrast.

`"Set1"`

Qualitative palette from RColorBrewer (up to 9 colors).

`"Set2"`

Softer qualitative palette (up to 8 colors).

`"Dark2"`

Darker qualitative palette (up to 8 colors).

`"Paired"`

Paired qualitative palette (up to 12 colors).

`"custom"`

Use a custom vector of colors via `custom_colors`.

custom_colors

A character vector of valid color strings (hex codes or R color names) used when `palette = "custom"`. The number of colors should match or exceed the number of spectra in the data. If fewer colors are provided than spectra, colors will be recycled with a warning.

Value

A `ggplot` object representing the spectral plot.

Examples

if (FALSE) { # \dontrun{
# Default viridis palette
spec_smartplot(spec_data, wn_col = "wavenumber")

# Built-in qualitative palette
spec_smartplot(spec_data, wn_col = "wavenumber", palette = "Set1")

# Custom colors
spec_smartplot(spec_data, wn_col = "wavenumber",
               palette = "custom",
               custom_colors = c("#E63946", "#457B9D", "#2A9D8F"))
} # }