chmLayer<- {NGCHM}

Set (or append) a specified Data Layer in an NG-CHM.

Description

This function sets a Data Layer in a Next Generation Clustered Heat Map.

Arguments

x

The NG-CHM object to set the data layer of

label

The name or index of the data layer to set. If a name, replace the layer with that name. Append a new layer if no layer with that name exists. If an index, replace the specified layer. If zero (0), prepend the new layer. If minus one (-1) or N+1 (for an NG-CHM with N layers), appends a new layer.

colors

A colormap for the new layer. If missing, defaults to the color map of the layer being replaced, or to the default new layer color map for a new layer.

summarizationMethod

The summarization method for the new layer. If missing, defaults to the summarization method of the layer being replaced, or to the default new layer summarization method for a new layer.

cuts_color

The cuts color for the new layer. If missing, defaults to the cuts color of the layer being replaced, or to the default cuts color for a new layer.

value

Either a matrix or a data layer to set in the NG-CHM. If value is a matrix, the other data layer parameters (label, colors, summarizationMethod, and cuts_color) are set from the parameters if specified, from the old data layer (if any), or the defaults for a new data layer (see chmNewDataLayer). If value is a data layer, any other data layer parameters specified will override those in the replacement layer.

Value

An object of class ngchm.

See Also

ngchmLayer

chmNewDataLayer

Examples

# If the NGCHMDemoData package is installed, use demo usage
if (requireNamespace("NGCHMDemoData", quietly = TRUE)) {
  data(TCGA.GBM.Demo, package = "NGCHMDemoData")
  matrix <- TCGA.GBM.ExpressionData[1:50, 1:50]
  hm <- chmNew("New Heat Map")
  chmLayer(hm, "Layer 1") <- matrix
  chmLayer(hm, 1, cuts_color = "#fefefe") <- chmNewDataLayer("New data layer", matrix + 1)
}
# Small example not requiring NGCHMDemoData
matrix <- matrix(rnorm(100),
  nrow = 10, ncol = 10,
  dimnames = list(paste0("r", 1:10), paste0("c", 1:10))
)
hm <- chmNew("New Heat Map")
chmLayer(hm, "Layer 1") <- matrix
chmLayer(hm, 1, cuts_color = "#fefefe") <- chmNewDataLayer("New data layer", matrix + 1)