For dendrogram based heat maps the
arguments are passed on to heatmap.2
in
gplots. See for example margins
and col
.
The following arguments for heatmap.2
cannot be used:
Rowv, Colv, hclustfun, reorderfun
.
For seriation-based heat maps further arguments include:
gp
an object of class gpar
containing graphical
parameters (see gpar
in package grid).
newpage
a logical indicating whether to start
plot on a new
page (see gpar
in package grid).
prop
a logical indicating whether the height and width of
x
should be plotted proportional to its dimensions.
showdist
Display seriated dissimilarity matrices? Values are "none"
, "both"
,
"rows"
or "columns"
.
key
logical; show a colorkey?.
- key.lab
string plotted next to the color key.
axes
one of "auto"
(default; show axis
labels if there are
less than 25 labels), "x"
, "y"
,
"both"
and "none"
.
margins
bottom and right-hand-side margins are
calculated automatically or can be specifies as a vector
of two numbers (in lines).
zlim
range of values displayed.
col
, col_dist
color palettes used.
For dendrogram = TRUE
, seriate.hclust
with the default method "optimal"
is used for arranging the
dendrograms and x
. heatmap
is used for plotting.
For dendrogram = FALSE
, seriate.dist
with the default method "tsp"
(a traveling salesperson solver) for arranging x
is used.
grid code implemented in this package
is used to produce the plot.
Note that unlike the default behavior of heatmap
,
scaling is not automatically applied. The data
have to be scaled before using hmap
.