interactive_plots: Interactive plots for OpenSpecy objects

In OpenSpecy: Analyze, Process, Identify, and Share Raman and (FT)IR Spectra

Interactive plots for OpenSpecy objects

Description

These functions generate heatmaps, spectral plots, and interactive plots for OpenSpecy data.

Usage

plotly_spec(x, ...)

## Default S3 method:
plotly_spec(x, ...)

## S3 method for class 'OpenSpecy'
plotly_spec(
  x,
  x2 = NULL,
  model = NULL,
  model_class = NULL,
  model_colorscale = list(c(0, "#d73027"), c(0.5, "#fee08b"), c(1, "#1a9850")),
  model_opacity = 0.28,
  line = list(color = "rgb(255, 255, 255)"),
  line2 = list(dash = "dot", color = "rgb(255,0,0)"),
  font = list(color = "#FFFFFF"),
  plot_bgcolor = "rgba(17, 0, 73, 0)",
  paper_bgcolor = "rgb(0, 0, 0)",
  showlegend = FALSE,
  make_rel = TRUE,
  ...
)

model_class_weights(model, model_class)

heatmap_spec(x, ...)

## Default S3 method:
heatmap_spec(x, ...)

## S3 method for class 'OpenSpecy'
heatmap_spec(
  x,
  z = NULL,
  sn = NULL,
  cor = NULL,
  min_sn = NULL,
  min_cor = NULL,
  select = NULL,
  font = list(color = "#FFFFFF"),
  plot_bgcolor = "rgba(17, 0, 73, 0)",
  paper_bgcolor = "rgb(0, 0, 0)",
  colorscale = "Viridis",
  showlegend = FALSE,
  type = "interactive",
  ...
)

interactive_plot(x, ...)

## Default S3 method:
interactive_plot(x, ...)

## S3 method for class 'OpenSpecy'
interactive_plot(
  x,
  x2 = NULL,
  select = NULL,
  line = list(color = "rgb(255, 255, 255)"),
  line2 = list(dash = "dot", color = "rgb(255,0,0)"),
  font = list(color = "#FFFFFF"),
  plot_bgcolor = "rgba(17, 0, 73, 0)",
  paper_bgcolor = "rgb(0, 0, 0)",
  colorscale = "Viridis",
  ...
)

Arguments

x	an OpenSpecy object containing metadata and spectral data for the first group.
x2	an optional second OpenSpecy object containing metadata and spectral data for the second group.
model	optional model library returned by train_spec_model(). Supplying this with model_class adds a logistic-regression coefficient background to plotly_spec().
model_class	exact trained class label whose signed logistic coefficients should be displayed. Positive weights are green, values near zero yellow, and negative weights red. These are model weights, not causal peak attributions.
model_colorscale	continuous Plotly colorscale for signed model weights, centered at zero.
model_opacity	opacity of the model-weight background from zero to one.
line	list; line parameter for x; passed to add_trace().
line2	list; line parameter for x2; passed to
font	list; passed to layout().
plot_bgcolor	color value; passed to layout().
paper_bgcolor	color value; passed to layout().
showlegend	whether to show the legend passed to
make_rel	logical, whether to make the spectra relative or use the raw values
z	optional numeric vector specifying the intensity values for the heatmap. If not provided, the function will use the intensity values from the OpenSpecy object.
sn	optional numeric value specifying the signal-to-noise ratio threshold. If provided along with min_sn, regions with SNR below the threshold will be excluded from the heatmap.
cor	optional numeric value specifying the correlation threshold. If provided along with min_cor, regions with correlation below the threshold will be excluded from the heatmap.
min_sn	optional numeric value specifying the minimum signal-to-noise ratio for inclusion in the heatmap. Regions with SNR below this threshold will be excluded.
min_cor	optional numeric value specifying the minimum correlation for inclusion in the heatmap. Regions with correlation below this threshold will be excluded.
select	optional index of the selected spectrum to highlight on the heatmap.
colorscale	colorscale passed to add_trace() can be an array or one of "Blackbody", "Bluered", "Blues", "Cividis", "Earth", "Electric", "Greens", "Greys", "Hot", "Jet", "Picnic", "Portland", "Rainbow", "RdBu", "Reds", "Viridis", "YlGnBu", "YlOrRd".
type	specification for plot type either interactive or static plot_ly().
...	further arguments passed to plot_ly().

Value

A plotly heatmap object displaying the OpenSpecy data. A subplot containing the heatmap and spectra plot. A plotly object displaying the spectra from the OpenSpecy object(s).

Author(s)

Win Cowger, Zacharias Steinmetz

Examples

if (interactive()) {
  data("raman_hdpe")
  tiny_map <- read_extdata("CA_tiny_map.zip") |> read_zip()
  plotly_spec(raman_hdpe)

  heatmap_spec(tiny_map, z = tiny_map$metadata$y, showlegend = TRUE)

  sample_spec(tiny_map, size = 12) |>
    interactive_plot(select = 2, x2 = raman_hdpe)
}

OpenSpecy documentation built on Oct. 6, 2026, 1:07 a.m.