heatmap.3 | R Documentation |
A modified version of heatmap.2 from the gplots package for cluster plotting
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 = min(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("column", "row", "both", "none"),
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("histogram", "density", "none"),
denscol = tracecol,
symkey = min(x < 0, na.rm = TRUE) || symbreaks,
densadj = 0.25,
main = NULL,
xlab = NULL,
ylab = NULL,
lmat = NULL,
lhei = NULL,
lwid = NULL,
...
)
x |
numeric matrix of the values to be plotted. |
Rowv |
determines if and how the row dendrogram should be
reordered. By default, it is TRUE, which implies dendrogram is
computed and reordered based on row means. If NULL or FALSE, then no
dendrogram is computed and no reordering is done. If a
|
Colv |
determines if and how the column dendrogram should
be reordered. Has the options as the |
distfun |
function used to compute the distance (dissimilarity)
between both rows and columns. Defaults to |
hclustfun |
function used to compute the hierarchical clustering
when |
dendrogram |
character string indicating whether to draw 'none', 'row', 'column' or 'both' dendrograms. Defaults to 'both'. However, if Rowv (or Colv) is FALSE or NULL and dendrogram is 'both', then a warning is issued and Rowv (or Colv) arguments are honoured. |
symm |
logical indicating if |
scale |
character indicating if the values should be centered and
scaled in either the row direction or the column direction, or
none. The default is |
na.rm |
logical indicating whether |
revC |
logical indicating if the column order should be
|
add.expr |
expression that will be evaluated after the call to
|
breaks |
(optional) Either a numeric vector indicating the
splitting points for binning |
symbreaks |
Boolean indicating whether breaks should be
made symmetric about 0. Defaults to |
col |
colors used for the image. Defaults to heat colors
( |
colsep , rowsep , sepcolor |
(optional) vector of integers
indicating which columns or rows should be separated from the
preceding columns or rows by a narrow space of color
|
sepwidth |
(optional) Vector of length 2 giving the width
(colsep) or height (rowsep) the separator box drawn by colsep and
rowsep as a function of the width (colsep) or height (rowsep) of a
cell. Defaults to |
cellnote |
(optional) matrix of character strings which will be placed within each color cell, e.g. p-value symbols. |
notecex |
(optional) numeric scaling factor for |
notecol |
(optional) character string specifying the color for
|
na.color |
Color to use for missing value ( |
trace |
character string indicating whether a solid "trace" line should be drawn across 'row's or down 'column's, 'both' or 'none'. The distance of the line from the center of each color-cell is proportional to the size of the measurement. Defaults to 'column'. |
tracecol |
character string giving the color for "trace" line. Defaults to "cyan". |
hline , vline , linecol |
Vector of values within cells where a
horizontal or vertical dotted line should be drawn. The color of
the line is controlled by |
margins |
numeric vector of length 2 containing the margins
(see |
ColSideColors |
(optional) character vector of length
|
RowSideColors |
(optional) character vector of length
|
cexRow , cexCol |
positive numbers, used as |
labRow , labCol |
character vectors with row and column labels to
use; these default to |
keysize |
numeric value indicating the size of the key |
density.info |
character string indicating whether to superimpose a 'histogram', a 'density' plot, or no plot ('none') on the color-key. |
denscol |
character string giving the color for the density
display specified by |
symkey |
Boolean indicating whether the color key should be
made symmetric about 0. Defaults to |
densadj |
Numeric scaling value for tuning the kernel width when
a density plot is drawn on the color key. (See the |
main , xlab , ylab |
main, x- and y-axis titles; defaults to none. |
lmat , lhei , lwid |
visual layout: position matrix, column height,
column width. See |
... |
additional arguments passed on to |
reorderfun |
|
srtRow , srtCol |
angle of row/column labels, in degrees from horizontal |
adjRow , adjCol |
2-element vector giving the (left-right, top-bottom) justification of row/column labels (relative to the text orientation). |
offsetRow , offsetCol |
Number of character-width spaces to place between row/column labels and the edge of the plotting region. |
colRow , colCol |
color of row/column labels, either a scalar to set the color of all labels the same, or a vector providing the colors of each label item |
key.title |
main title of the color key. If set to NA no title will be plotted. |
key.xlab |
x axis label of the color key. If set to NA no label will be plotted. |
key.ylab |
y axis label of the color key. If set to NA no label will be plotted. |
key.xtickfun |
function computing tick location and labels for
the xaxis of the color key. Returns a named list containing
parameters that can be passed to |
key.ytickfun |
function computing tick location and labels for
the y axis of the color key. Returns a named list containing
parameters that can be passed to |
key.par |
graphical parameters for the color key. Named list that
can be passed to |
extrafun |
A function to be called after all other work. See codegplots::heatmap.2. |
a base R plot
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