sarp.snowprofile.alignment (version 1.0.2)

plotSPalignment: Align and plot two snow profiles using DTW

Description

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.

Usage

plotSPalignment(
  query,
  ref,
  dtwAlignment = NULL,
  open.end = TRUE,
  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,
  ...
)

Arguments

query

The query snowprofile to be warped

ref

The reference snowprofile to be warped against

dtwAlignment

dtwSP object (optional)

open.end

Is an open end alignment desired? boolean

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 distMatSP)

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 plot.snowprofile

emphasizeLayers_ref

emphasize Layers in reference, see plot.snowprofile

...

Arguments passed to distMatSP and dtwSP

Value

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

Examples

# NOT RUN {
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"))


# }