plotly_spec {OpenSpecy}

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,
  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,
  ...
)

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,
  ...
)

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.

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 plot_ly().

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".

...

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

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)