bootstrapBlobs {Racmacs}

Calculate bootstrap blob data for an antigenic map

Description

This function takes a map for which the function bootstrapMap() has already been applied and draws contour blobs for each point illustrating how point position varies in each bootstrap repeat. The blobs are calculated using kernal density estimates according to these point distribution and drawn so as to encompass a given proportion of this variation according to the parameter conf.level. A conf.level set at 0.95 for example will draw blobs that are calculated to encompass 95% of the positional variation seen in the bootstrap repeats. Note however that the accuracy of these estimates will depend on the number of bootstrap repeats performed, for example whether 100 or 1000 repeats were performed in the initial calculations using bootstrapMap().

Usage

bootstrapBlobs(
  map,
  conf.level = 0.68,
  smoothing = 6,
  gridspacing = 0.25,
  antigens = TRUE,
  sera = TRUE,
  method = "ks"
)

Arguments

map

The acmap data object

conf.level

The proportion of positional variation captured by each blob

smoothing

The amount of smoothing to perform when performing the kernel density estimate, larger equates to more smoothing

gridspacing

grid spacing to use when calculating blobs, smaller values will produce more accurate blobs with smoother edges but will take longer to calculate.

antigens

Should blobs be calculated for antigens

sera

Should blobs be calculated for sera

method

One of "MASS", the default, or "ks", specifying the algorithm to use when calculating blobs in 2D. 3D will always use ks::kde.

Value

Returns an acmap object that will then show the corresponding bootstrap blobs when viewed or plotted.

See Also

Other map diagnostic functions: agCohesion(), bootstrapMap(), checkHemisphering(), dimensionTestMap(), logtiterTable(), map-table-distances, mapBootstrapCoords, mapDistances(), mapRelaxed(), mapResiduals(), pointStress, ptBootstrapBlob, ptBootstrapCoords(), ptLeverage, ptTriangulationBlob, recalculateStress(), stressTable(), tableColbases(), tableDistances(), triangulationBlobs(), unstableMaps