Usage
visHeatmap(data, scale = c("none", "row", "column"), row.metric =
c("none",
"pearson", "spearman", "kendall", "euclidean", "manhattan", "cos",
"mi"),
row.method = c("ward", "single", "complete", "average", "mcquitty",
"median", "centroid"), column.metric = c("none", "pearson", "spearman",
"kendall", "euclidean", "manhattan", "cos", "mi"), column.method =
c("ward",
"single", "complete", "average", "mcquitty", "median", "centroid"),
colormap = c("bwr", "jet", "gbr", "wyr", "br", "yr", "rainbow", "wb"),
ncolors = 64, zlim = NULL, row.cutree = NULL,
row.colormap = c("rainbow"), column.cutree = NULL,
column.colormap = c("rainbow"), ...)
Arguments
data
an input gene-sample data matrix used for
heatmap
scale
a character indicating when the input matrix
should be centered and scaled. It can be one of "none"
(no scaling), "row" (being scaled in the row direction),
"column" (being scaled in the column direction)
row.metric
distance metric used to calculate the
distance metric between rows. It can be one of "none"
(i.e. no dendrogram between rows), "pearson", "spearman",
"kendall", "euclidean", "manhattan", "cos" and "mi". See
details at
http://suprahex.r-forge.r-project.org/sDistance.html row.method
the agglomeration method used to
cluster rows. This should be one of "ward", "single",
"complete", "average", "mcquitty", "median" or
"centroid". See 'Note' below for details
column.metric
distance metric used to calculate
the distance metric between columns. It can be one of
"none" (i.e. no dendrogram between rows), "pearson",
"spearman", "kendall", "euclidean", "manhattan", "cos"
and "mi". See details at
http://suprahex.r-forge.r-project.org/sDistance.html column.method
the agglomeration method used to
cluster columns. This should be one of "ward", "single",
"complete", "average", "mcquitty", "median" or
"centroid". See 'Note' below for details
colormap
short name for the colormap. It can be
one of "jet" (jet colormap), "bwr" (blue-white-red
colormap), "gbr" (green-black-red colormap), "wyr"
(white-yellow-red colormap), "br" (black-red colormap),
"yr" (yellow-red colormap), "wb" (white-black colormap),
and "rainbow" (rainbow colormap, that is,
red-yellow-green-cyan-blue-magenta). Alternatively, any
hyphen-separated HTML color names, e.g.
"blue-black-yellow", "royalblue-white-sandybrown",
"darkgreen-white-darkviolet". A list of standard color
names can be found in
http://html-color-codes.info/color-names ncolors
the number of colors specified over the
colormap
zlim
the minimum and maximum z/patttern values for
which colors should be plotted, defaulting to the range
of the finite values of z. Each of the given colors will
be used to color an equispaced interval of this range.
The midpoints of the intervals cover the range, so that
values just outside the range will be plotted
row.cutree
an integer scalar specifying the
desired number of groups being cut from the row
dendrogram. Note, this optional is only enabled when the
row dengrogram is built
row.colormap
short name for the colormap to
color-code the row groups (i.e. sidebar colors used to
annotate the rows)
column.cutree
an integer scalar specifying the
desired number of groups being cut from the column
dendrogram. Note, this optional is only enabled when the
column dengrogram is built
column.colormap
short name for the colormap to
color-code the column groups (i.e. sidebar colors used to
annotate the columns)
...
additional graphic parameters. Type ?heatmap
for the complete list.