plotSPalignment: Align and plot two snow profiles using DTW

In sarp.snowprofile.alignment: Snow Profile Alignment, Aggregation, and Clustering

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,
  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 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
failureLayers_qu	draw arrow to failure layers (see plot.snowprofile)? provide height vector.
failureLayers_qu_col	color of arrow(s) (individual color string or vector, 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)

Author(s)

fherla

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"))

sarp.snowprofile.alignment documentation built on Aug. 8, 2022, 1:05 a.m.