bdm.qMap: ptSNE quantile-maps

In jgarriga65/bigMap: Big Data Mapping

ptSNE quantile-maps

Description

Maps quantitative variables onto the embedding space.

Usage

bdm.qMap(
  bdm,
  data,
  labels = NULL,
  subset = NULL,
  qMap.levels = 8,
  qMap.cex = 0.3,
  qMap.bg = "#FFFFFF",
  class.pltt = NULL,
  qtitle = NULL,
  cex.main = 1,
  colorbar = T,
  layer = 1
)

Arguments

bdm	A bdm instance as generated by bdm.init().
data	A matrix/data.frame to be mapped.
labels	A length nrow(bdm$data) vector of class labels to overlay onto the embedding. Label values are factorized as as.numeric(as.factor(labels)). Default value is labels = NULL.
subset	A numeric vector with the indexes of a subset of data. Data-points in the subset are heat-mapped and the rest are shown in light grey. By default all data-points are heat-mapped.
qMap.levels	The number of levels of the quantile-map (8 by default).
qMap.cex	The size of the data-points (as in par()).
qMap.bg	The background colour of the qMap plot. Default value is ptsne.bg = #FFFFFF (white).
class.pltt	If !is.null(labels) or !is.null(bdm$lbls), a colour palette to show class labels with the qMap plots. By default (qMap.pltt = NULL) the default palette is used.
qtitle	A vector of strings with titles for the plots. Default value is qtitle=NULL.
cex.main	The font size of the title (as in par()).
colorbar	A logical value (TRUE by default). FALSE hides the side colorbar.
layer	The number of a layer (1 by default).

Details

This is not a heat-map but a quantile-map plot. This function splits the range of each variable into as many quantiles as specified by levels so that the color gradient will hardly ever correspond to a constant numeric gradient. Thus, the mapping will show more evenly distributed colors though at the expense of possibly exaggerating artifacts. For variables with very extrem distributions, it will be impossible to find as many quantiles as desired and the distribution of colors will not be so homogeneous.

Value

None.

Examples

bdm.example()
bdm.qMap(ex$map, ex$data)
# --- show only components (1, 2, 4, 8) of the GMM
bdm.qMap(ex$map, ex$data, subset = which(ex$map$lbls %in% c(1, 4, 8, 16)))

jgarriga65/bigMap documentation built on June 10, 2024, 7:05 a.m.