plotCostDensitySP: Plot alignment cost density and warping path

Description Usage Arguments Note Author(s) Examples

View source: R/plotCostDensitySP.R

Description

Plot alignment cost density and warping path, optionally with the two snow profiles plotted in the margins along the axes.

Usage

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plotCostDensitySP(
  alignment,
  localCost = TRUE,
  labelHeight = FALSE,
  marginalPros = TRUE,
  pathCol = "black",
  target = FALSE,
  movingTarget = FALSE,
  tlty = "dotted",
  tlwd = 1.5,
  tcol = "black",
  tcex = 1.5,
  cex.lab = 1,
  xlab = NULL,
  ylab = NULL,
  ...
)

Arguments

alignment

object from dtwSP

localCost

plot local cost matrix, otherwise plot accumulated global cost.

labelHeight

plot axes in units of height (cm) or in unitless (i.e., layer index).

marginalPros

plot profiles in margins along the axes. default TRUE

pathCol

color of warping path

target

draw horizontal & vertical lines from matrix cells to corresponding layers in the (marginal) profiles. Provide either a vector of length 1 (i.e., index of warping path) or length 2 (i.e., x, y coordinates in terms of layer indices), or a matrix with 2 columns, specifying (x, y) if you desire multiple 'targets'

movingTarget

Do you want to draw the warping path only partially, from the origin to the target cross? Only possible if target cross is given as a scalar! default = FALSE (Useful to create GIF animations of a moving path)

tlty

target lty

tlwd

target lwd

tcol

target col

tcex

target cex

cex.lab

cex of axis labels (cf. par)

xlab

x-axis label to change default labeling

ylab

y-axis label to change default labeling

...

forwarded to par

Note

If you can't see the axis labels, try e.g., par(oma = c(3, 3, 0, 0)) before calling the function. Note, there seems to be a problem (only sometimes) with the left-hand labels that are for some reason not plotted parallel to the axis. Also, the routine is not bulletproof with respect to drawing 'targets'. Apologies for any inconveniences!

Author(s)

fherla

Examples

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## first align profiles:
dtwAlignment <- dtwSP(SPpairs$A_modeled, SPpairs$A_manual, open.end = FALSE)

## then plot cost density:
plotCostDensitySP(dtwAlignment)

## label height instead of layer index, and don't show warping path:
plotCostDensitySP(dtwAlignment, labelHeight = TRUE, pathCol = "transparent")

## draw lines to the cell that corresponds to the DH and SH layers
plotCostDensitySP(dtwAlignment, target = c(191, 208))

## "moving target", i.e., draw warping path only from origin to target:
plotCostDensitySP(dtwAlignment, target = 200, movingTarget = TRUE)
plotCostDensitySP(dtwAlignment, target = 266, movingTarget = TRUE)


## A cool GIF can be created from frames like those
create_GIF <- FALSE
if (create_GIF){
  nPath <- length(dtwAlignment$index1)
  resolution <- 100  # i.e. super low, make value smaller for smoother GIF
  for (k in seq(1, nPath, by = resolution)) {
    plotCostDensitySP(dtwAlignment, target = k, movingTarget = TRUE)
  }
}

sarp.snowprofile.alignment documentation built on Dec. 3, 2020, 9:08 a.m.