Interactive plots for OpenSpecy objects — plotly

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,
  make_rel = TRUE,
  ...
)

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.
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

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)