plotSPalignment function

Align and plot two snow profiles using DTW

This is a plotting routine for the DTW alignment of two snow profiles. Either provide two snow profiles or a dtwSP alignment object. Don't resize the figure, otherwise the plotted alignment segments will not be in correct place anymore! If you need a specific figure size, use grDevices::png with a width/height aspect ratio of about 5/3.

plotSPalignment(
  query,
  ref,
  dtwAlignment = NULL,
  keep.alignment = FALSE,
  plot.costDensity = FALSE,
  plot.warpedQuery = TRUE,
  label.ddate = FALSE,
  segCol = "gray70",
  segLty = "dotted",
  segLwd = 1,
  segTidy = FALSE,
  segInd = TRUE,
  segEmph = NA,
  cex = 1,
  mainQu = "query",
  mainRef = "reference",
  mainQwarped = "warped query",
  emphasizeLayers_qu = FALSE,
  emphasizeLayers_ref = FALSE,
  failureLayers_qu = FALSE,
  failureLayers_qu_col = "red",
  ...
)

Arguments

• query: The query snowprofile to be warped
• ref: The reference snowprofile to be warped against
• dtwAlignment: dtwSP object (optional)
• keep.alignment: Return dtwSP object with resampled query, ref and warped query? boolean
• plot.costDensity: First graph, plotCostDensitySP with warping path? boolean, default = FALSE
• plot.warpedQuery: plot warped query additionally to query, ref and alignment segments? (i.e. three pane plot) boolean, default = TRUE
• label.ddate: Label deposition date in profiles? (Only possible if ddate is given in 'dims', cf distanceSPlayers )
• segCol: Color of alignment segments. Passed to gpar , default = "gray70"
• segLty: Linestyle of alignment segments. Passed to gpar , default = "dotted"
• segLwd: Linewidth of alignment segments, default = 1
• segTidy: Tidy up alignment segments, if profiles have not been resampled? boolean, default FALSE i.e. one segment line per (synthetic) layer interface -> supports visual understanding of alignment, but is also often confusing (segTidy currently only implemented for tidying up to gtype and hardness interfaces)
• segInd: Index vector of query layers that will get alignment segments drawn. Note, that the profiles might get resampled, so pre-calculate your correct indices!
• segEmph: Index vector of query layers, the alignment segments of which will be emphasized (thick and red). Note, that the profiles might get resampled, so pre-calculate your correct indices!
• cex: font size, cf. par
• mainQu: subtitle for query subfigure
• mainRef: subtitle for reference subfigure
• mainQwarped: subtitle for warped query subfigure
• emphasizeLayers_qu: emphasize Layers in query, see sarp.snowprofile::plot.snowprofile
• emphasizeLayers_ref: emphasize Layers in reference, see sarp.snowprofile::plot.snowprofile
• failureLayers_qu: draw arrow to failure layers (see sarp.snowprofile::plot.snowprofile )? provide height vector.
• failureLayers_qu_col: color of arrow(s) (individual color string or vector, see sarp.snowprofile::plot.snowprofile )
• ...: Arguments passed to distanceSPlayers and dtwSP

Returns

dtw object with the resampled '$query' and '$reference', as well as the warped query '$queryWarped' (only if keep.alignment is TRUE)

Examples

plotSPalignment(SPpairs$B_modeled1, SPpairs$B_modeled2)

plotSPalignment(SPpairs$B_modeled1, SPpairs$B_modeled2, dims = c("gtype"), weights = c(1))

## alternatively keep alignment:
alignment <- plotSPalignment(SPpairs$B_modeled1, SPpairs$B_modeled2, keep.alignment = TRUE)
print(paste("Similarity between profiles:", alignment$sim))

## alternatively, with precomputed alignment and emphasized layer matches:
dtwAlignment <- dtwSP(SPpairs$A_modeled, SPpairs$A_manual, open.end = FALSE)
plotSPalignment(dtwAlignment = dtwAlignment, segEmph = c(190, 192))

## directly after plotting, add text to figure:
grid::grid.text("Profiles SPpairs$A (modeled/manual)", x = 0.5, y = 0.8,
                gp = grid::gpar(fontsize=12, col="grey"))

Author(s)

fherla