- Matrix
numerical matrix to be plotted in the heatmap.
- xLabels
labels for the columns. See Details.
- yLabels
labels for the rows. See Details.
- xSymbols
additional labels used when xLabels are interpreted as colors. See Details.
- ySymbols
additional labels used when yLabels are interpreted as colors. See Details.
- colorLabels
logical: should xLabels and yLabels be interpreted as colors? If
given, overrides xColorLabels and yColorLabels below.
- xColorLabels
logical: should xLabels be interpreted as colors?
- yColorLabels
logical: should yLabels be interpreted as colors?
- checkColorsValid
logical: should given colors be checked for validity
against the output of colors() ? If this argument is FALSE, invalid color specification
will trigger an error.
- invertColors
logical: should the color order be inverted?
- setStdMargins
logical: should standard margins be set before calling the plot function?
Standard margins depend on colorLabels: they are wider for text labels and narrower for color
labels. The defaults are static, that is the function does not attempt to guess the optimal margins.
- xLabelsPosition
a character string specifying the position of labels for the columns.
Recognized values are (unique abbreviations of) "top", "bottom".
- xLabelsAngle
angle by which the column labels should be rotated.
- xLabelsAdj
justification parameter for column labels. See par and the
description of parameter "adj".
- yLabelsPosition
a character string specifying the position of labels for the columns.
Recognized values are (unique abbreviations of) "left", "right".
- xColorWidth
width of the color labels for the x axis expressed in user corrdinates.
- yColorWidth
width of the color labels for the y axis expressed in user coordinates.
- xColorOffset
gap between the y axis and color labels, in user coordinates.
- yColorOffset
gap between the x axis and color labels, in user coordinates.
- colorMatrix
optional explicit specification for the color of the heatmap cells. If given, overrides values
specified in colors and naColor.
- colors
color pallette to be used in the heatmap. Defaults to heat.colors. Only used if
colorMatrix is not given.
- naColor
color to be used for encoding missing data. Only used if colorMatrix is not used.
- textMatrix
optional text entries for each cell. Either a matrix of the same dimensions as
Matrix or a vector of the same length as the number of entries in Matrix.
- cex.text
character expansion factor for textMatrix.
- textAdj
Adjustment for the entries in the text matrix. See the adj argument to
text.
- cex.lab
character expansion factor for text labels labeling the axes.
- cex.lab.x
character expansion factor for text labels labeling the x axis. Overrides cex.lab
above.
- cex.lab.y
character expansion factor for text labels labeling the y axis. Overrides cex.lab
above.
- colors.lab.x
colors for character labels or symbols along x axis.
- colors.lab.y
colors for character labels or symbols along y axis.
- font.lab.x
integer specifying font for labels or symbols along x axis. See text.
- font.lab.y
integer specifying font for labels or symbols along y axis. See text.
- bg.lab.x
background color for the margin along the x axis.
- bg.lab.y
background color for the margin along the y axs.
- x.adj.lab.y
Justification of labels for the y axis along the x direction. A value of 0
produces left-justified text, 0.5 (the default) centered
text and 1 right-justified text.
- plotLegend
logical: should a color legend be plotted?
- keepLegendSpace
logical: if the color legend is not drawn, should the space be left empty
(TRUE), or should the heatmap fill the space (FALSE)?
- legendLabel
character string to be shown next to the label analogous to an axis label.
- cex.legendLabel
character expansion factor for the legend label.
- verticalSeparator.x
indices of columns in input Matrix after
which separator lines (vertical lines between columns)
should be drawn. NULL means no lines will be drawn.
- verticalSeparator.col
color(s) of the vertical separator lines. Recycled if need be.
- verticalSeparator.lty
line type of the vertical separator lines. Recycled if need be.
- verticalSeparator.lwd
line width of the vertical separator lines. Recycled if need be.
- verticalSeparator.ext
number giving the extension of the separator line into the margin as a fraction
of the margin width. 0 means no extension, 1 means extend all the way through the margin.
- verticalSeparator.interval
number giving the interval for vertical separators. If larger than zero, vertical
separators will be drawn after every verticalSeparator.interval of displayed columns.
Used only when length of verticalSeparator.x is zero.
- horizontalSeparator.y
indices of columns in input Matrix after which separator lines (horizontal lines
between columns) should be drawn. NULL means no lines will be drawn.
- horizontalSeparator.col
color(s) of the horizontal separator lines. Recycled if need be.
- horizontalSeparator.lty
line type of the horizontal separator lines. Recycled if need be.
- horizontalSeparator.lwd
line width of the horizontal separator lines. Recycled if need be.
- horizontalSeparator.ext
number giving the extension of the separator line into the margin as a
fraction of the margin width. 0 means no extension, 1 means extend all the way through the margin.
- horizontalSeparator.interval
number giving the interval for horizontal separators. If larger than zero, horizontal
separators will be drawn after every horizontalSeparator.interval of displayed rows.
Used only when length of horizontalSeparator.y is zero.
- showRows
A numeric vector giving the indices of rows that are actually to be shown. Defaults to all rows.
- showCols
A numeric vector giving the indices of columns that are actually to be shown. Defaults to all columns.
- ...
other arguments to function heatmap.