heatmap.3: A function that creates a dataframe to be used as input to...

In mssm-msf-2019/BiostatsALL:

Description

This function given a numeric matrix returns a data frame with the necessary information to create a heatmap with specifics features

Usage

heatmap.3(x, Rowv = TRUE, Colv = if (symm) "Rowv" else TRUE,
  distfun = dist, hclustfun = hclust, dendrogram = c("both", "row",
  "column", "none"), symm = FALSE, scale = c("none", "row", "column"),
  na.rm = TRUE, revC = identical(Colv, "Rowv"), add.expr, breaks,
  symbreaks = max(x < 0, na.rm = TRUE) || scale != "none",
  col = "heat.colors", colsep, rowsep, sepcolor = "white",
  sepwidth = c(0.05, 0.05), cellnote, notecex = 1, notecol = "cyan",
  na.color = par("bg"), trace = c("none", "column", "row", "both"),
  tracecol = "cyan", hline = median(breaks), vline = median(breaks),
  linecol = tracecol, margins = c(5, 5), ColSideColors, RowSideColors,
  side.height.fraction = 0.3, cexRow = 0.2 + 1/log10(nr), cexCol = 0.2 +
  1/log10(nc), labRow = NULL, labCol = NULL, key = TRUE, keysize = 1.5,
  density.info = c("none", "histogram", "density"), denscol = tracecol,
  symkey = max(x < 0, na.rm = TRUE) || symbreaks, densadj = 0.25,
  main = NULL, xlab = NULL, ylab = NULL, lmat = NULL, lhei = NULL,
  lwid = NULL, NumColSideColors = 1, NumRowSideColors = 1,
  KeyValueName = "Value", ...)

Arguments

x	numeric matrix
Rowv	determines if and how the row dendrogram should be computed and reordered. Either a dendrogram or a vector of values used to reorder the row dendrogram or NA to suppress any row dendrogram (and reordering) or by default, NULL. It is TRUE by default.
Colv	determines if and how the column dendrogram should be reordered. Has the same options as the Rowv argument above and additionally when x is a square matrix, Colv = "Rowv" means that columns should be treated identically to the rows (and so if there is to be no row dendrogram there will not be a column one either). By defaulf: if (symm) "Rowv" else TRUE.
distfun	function used to compute the distance (dissimilarity) between both rows and columns. Defaults to dist.
hclustfun	function used to compute the hierarchical clustering when Rowv or Colv are not dendrograms. Defaults to hclust. Should take as argument a result of distfun and return an object to which as.dendrogram can be applied.
dendrogram	dendrogram and weights for reordering the row and column dendrograms. Defaults to c("both","row", "column", "none").
symm	logical indicating if x should be treated symmetrically; can only be true when x is a square matrix. Defaults on FALSE.
scale	character vector indicating if the values should be centered and scaled in either the row direction or the column direction, or none. The default is c("none","row", "column").
na.rm	logical indicating whether NA's should be removed. Default is TRUE.
revC	= identical(Colv,"Rowv")
add.expr
breaks
symbreaks	= max(x < 0, na.rm = TRUE) || scale != "none"
col	= "heat.colors"
colsep
rowsep
sepcolor	= "white"
sepwidth	= c(0.05, 0.05)
cellnote,
notecex	= 1
notecol	= "cyan"
na.color	= par("bg")
trace	= c("none", "column","row", "both")
tracecol	= "cyan"
hline	= median(breaks)
vline	= median(breaks)
linecol	= tracecol
margins	= c(5,5)
ColSideColors
RowSideColors
cexRow	= 0.2 + 1/log10(nr)
cexCol	= 0.2 + 1/log10(nc)
labRow	= NULL
labCol	= NULL
key	= TRUE
keysize	= 1.5
density.info	= c("none", "histogram", "density")
denscol	= tracecol
symkey	= max(x < 0, na.rm = TRUE) || symbreaks, densadj = 0.25
main	= NULL, xlab = NULL
ylab	= NULL, lmat = NULL
lhei	= NULL, lwid = NULL
NumColSideColors	= 1
NumRowSideColors	= 1
side.height.fraction=0.3
KeyValueName="Value"

Examples

heatmap.3(x, Rowv = TRUE, Colv = if (symm) "Rowv" else TRUE,
distfun = dist, hclustfun = hclust, dendrogram = c("both","row", "column", "none"),
symm = FALSE, scale = c("none","row", "column"), na.rm = TRUE, revC = identical(Colv,"Rowv"),
add.expr,   breaks,   symbreaks = max(x < 0, na.rm = TRUE) || scale != "none",
col = "heat.colors",  colsep, rowsep, sepcolor = "white", sepwidth = c(0.05, 0.05),
cellnote,   notecex = 1,  notecol = "cyan", na.color = par("bg"),trace = c("none", "column","row", "both"),
tracecol = "cyan", hline = median(breaks), vline = median(breaks), linecol = tracecol,
margins = c(5,5), ColSideColors,RowSideColors,side.height.fraction=0.3,
cexRow = 0.2 + 1/log10(nr),cexCol = 0.2 + 1/log10(nc),
labRow = NULL, labCol = NULL, key = TRUE, keysize = 1.5,
density.info = c("none", "histogram", "density"), denscol = tracecol,
symkey = max(x < 0, na.rm = TRUE) || symbreaks, densadj = 0.25,
main = NULL, xlab = NULL, ylab = NULL, lmat = NULL, lhei = NULL, lwid = NULL,
NumColSideColors = 1, NumRowSideColors = 1, KeyValueName="Value",...)

mssm-msf-2019/BiostatsALL documentation built on May 22, 2019, 12:16 p.m.