prepare_heatmap_data2: Function to prepare data for a heatmap: scaling, dendrograms,...
In heatmapFlex: Tools to Generate Flexible Heatmaps

Description Usage Arguments Details

View source: R/heatmap.n2.R

Function to prepare data for a heatmap: scaling, dendrograms, ...

prepare_heatmap_data2(
  x,
  labRow = NA,
  labCol = NA,
  Rowv = NULL,
  Colv = NULL,
  reorder = c(TRUE, TRUE),
  distfun = dist,
  hclustfun = hclust,
  rowMembers = NULL,
  colMembers = NULL,
  spacer = 1,
  scale = "none",
  trim = NULL,
  zlim = NULL,
  col = NULL,
  filter = c(TRUE, TRUE),
  add.sig = FALSE,
  pv = NULL
)

`x`	(`numeric`). Numeric matrix.
`labRow`	(`character`). Custom row labels.
`labCol`	(`character`). Custom column labels.
`Rowv`	(`dendrogram` or `integer`). Custom dendrogram object or integer vector giving the ordering index for rows.
`Colv`	(`dendrogram` or `integer`). Custom dendrogram object or integer vector giving the ordering index for columns
`reorder`	(`logical`). Boolean of length 2 for rows and columns. Should rows and/or columns be reordered according to `Rowv`/`Colv`?
`distfun`	(`function`). Distance function. Defaults to `dist`.
`hclustfun`	(`function`). Hierarchical clustering function. Defaults to `hclust`.
`rowMembers`	(`character`). Group vector to split rows by.
`colMembers`	(`character`). Group vector to split columns by.
`spacer`	(`integer`). Length 1 integer used as spacer to separate groups (see `rowMembers`/`colMembers`). Defaults to 1.
`scale`	(`character`). One of "row", "column" or "none": By which dimension should data be scaled? Defaults to "none".
`trim`	(`numeric`). Value to "cut off" data distribution. Values and both ends of the distribution, larger or smaller, respectively, will be made equal to `+/-trim`. Defaults to `NULL`, no trimming.
`zlim`	(`numeric`). Value to set the ranges for plotting `x` and `y` values. Supports both symmetrical (with default `NULL`) and asymmetrical (`NA`) automatic `zlim.` Used for zooming.
`col`	(`character`) Name (acronym) of the colour palette to use. Can be one of "RdBkGn" (c("green", "black", "red")), "BuYl" (c("blue", "yellow")), "BuWtRd" (c("blue", "white", "red")) or a valid name used by `brewer.pal`. Defaults to NULL which will set "RdBkGn".
`filter`	(`integer` or `logical`.) For filtering rows/columns: TRUE (=1.0) = remove rows/columns with only NAs, 0.5 = remove if >= 50 per cent NAs, etc. Defaults to `c(TRUE, TRUE)`.
`add.sig`	(`logical`). Should significance asterixes be drawn?
`pv`	(`numeric`). Matrix of the same dimensions as `x` with P-Values for correlation significance.

This function is used by heatmap.n2 and should not be called bu the user directly. It is only documented because its arguments are passed by the main function when given there.

heatmapFlex documentation built on Aug. 19, 2021, 9:07 a.m.