Set the color mapping of a numerical vector, and the tick and tick labels of its legend

The purpose of this function is to auto-handle outliers in the numerical vectors, because outliers compress the color mapping and make it difficult to distinguish among the values of non-outliers.Here are the ways to achieve that goal in this function if outliers are present:

only non-outliers are used in color-value mapping.
a '<' or '>' sign is prefixed to the first or last tick labels.

Usage

setColMapAndLegend(
  vec,
  colMap = NULL,
  whiteValue = NA,
  intAsDiscreteCutoff = 6,
  rmLegendOutliers = T,
  isAnnotation = F,
  legendTicks = NULL,
  legendTickLabels = NULL
)

Arguments

vec: numerical; a vector or matrix
colMap: a named numerical vector for the color mapping,NULL; if colMap is not provided, the names of colMap is set as the followings: * if isAnnotation, c('white',x) where x is a random color from getDistinctColors. * otherwise, c('green4', 'white', 'red').
whiteValue: Numeric, NA; it is the value of the white or middle color in the legend if colMap consists of three colors representing, e.g. up, no change, down, etc.
intAsDiscreteCutoff: integer, 6; if mat1 is an integer matrix and has < 6 unique values, the color mapping in the legend will be discrete.
rmLegendOutliers: logical, TRUE; If colMap is not provided, if FALSE, the range of legend ticks covers all values of vac if TRUE, the range of legend ticks covers only non-outliers
isAnnotation: logical, FALSE; if TRUE, the legend is for the annotation of a heatmap, not for heatmap itself;
legendTicks: numerical vector, NULL;
legendTickLabels: character vector, NULL;

Value

a list of following items

colmap: the completed colMap
legendParas: list(at = legendTicks,labels = legendTickLabels). it may also contains legend_gp if vec is discrete integers; passed to ComplexHeatmap::HeatmapAnnotation(annotation_legend_param)
newVals: infinite values in vec, if present, are set to NA
isDiscrete: is vec discrete?

Examples

# none