Heatmaps of NMF Factors
basismap(object, ...)
## S4 method for signature 'NMF'
basismap(object, color = "YlOrRd:50",
scale = "r1", Rowv = TRUE, Colv = NA,
subsetRow = FALSE, annRow = NA, annCol = NA,
tracks = "basis", main = "Basis components",
info = FALSE, ...)
coefmap(object, ...)
## S4 method for signature 'NMF'
coefmap(object, color = "YlOrRd:50",
scale = "c1", Rowv = NA, Colv = TRUE, annRow = NA,
annCol = NA, tracks = "basis",
main = "Mixture coefficients", info = FALSE, ...)
consensusmap(object, ...)
## S4 method for signature 'NMFfitX'
consensusmap(object, annRow = NA,
annCol = NA,
tracks = c("basis:", "consensus:", "silhouette:"),
main = "Consensus matrix", info = FALSE, ...)
## S4 method for signature 'matrix'
consensusmap(object,
color = "-RdYlBu",
distfun = function(x) as.dist(1 - x),
hclustfun = "average", Rowv = TRUE, Colv = "Rowv",
main = if (is.null(nr) || nr > 1) "Consensus matrix" else "Connectiviy matrix",
info = FALSE, ...)
## S4 method for signature 'NMFfitX'
coefmap(object, Colv = TRUE,
annRow = NA, annCol = NA,
tracks = c("basis", "consensus:"), ...)object |
an object from which is extracted NMF factors or a consensus matrix |
... |
extra arguments passed to
|
subsetRow |
Argument that specifies how to filter
the rows that will appear in the heatmap. When
|
tracks |
Special additional annotation tracks to highlight associations between basis components and sample clusters:
|
info |
if |
color |
colour specification for the heatmap. Default to palette '-RdYlBu2:100', i.e. reversed palette 'RdYlBu2' (a slight modification of RColorBrewer's palette 'RdYlBu') with 100 colors. Possible values are:
When the coluor palette is specified with a single value, and is negative or preceded a minus ('-'), the reversed palette is used. The number of breaks can also be specified after a colon (':'). For example, the default colour palette is specified as '-RdYlBu2:100'. |
scale |
character indicating how the values should scaled in either the row direction or the column direction. Note that the scaling is performed after row/column clustering, so that it has no effect on the row/column ordering. Possible values are:
|
Rowv |
clustering specification(s) for the rows. It allows to specify the distance/clustering/ordering/display parameters to be used for the rows only. Possible values are:
|
Colv |
clustering specification(s) for the columns.
It accepts the same values as argument |
annRow |
specifications of row annotation tracks
displayed as coloured columns on the left of the
heatmaps. The annotation tracks are drawn from left to
right. The same conversion, renaming and colouring rules
as for argument |
annCol |
specifications of column annotation tracks
displayed as coloured rows on top of the heatmaps. The
annotation tracks are drawn from bottom to top. A single
annotation track can be specified as a single vector;
multiple tracks are specified as a list, a data frame, or
an ExpressionSet object, in which case the
phenotypic data is used ( |
main |
Main title as a character string or a grob. |
distfun |
default distance measure used in clustering rows and columns. Possible values are:
|
hclustfun |
default clustering method used to cluster rows and columns. Possible values are: |
IMPORTANT: although they essentially have the
same set of arguments, their order sometimes differ
between them, as well as from aheatmap. We
therefore strongly recommend to use fully named arguments
when calling these functions.
basimap default values for the following arguments
of aheatmap:
the color palette;
the scaling specification, which by
default scales each row separately so that they sum up to
one (scale='r1');
the column ordering which is disabled;
allowing for passing feature
extraction methods in argument subsetRow, that are
passed to extractFeatures. See argument
description here and therein.
the addition of a default named annotation track, that shows the dominant basis component for each row (i.e. each feature).
This track is specified in argument tracks (see
its argument description). By default, a matching column
annotation track is also displayed, but may be disabled
using tracks=':basis'.
a suitable title and extra information like the
fitting algorithm, when object is a fitted NMF
model.
coefmap redefines default values for the following
arguments of aheatmap:
the color palette;
the scaling specification, which by
default scales each column separately so that they sum up
to one (scale='c1');
the row ordering which is disabled;
the addition of a default annotation track, that shows the most contributing basis component for each column (i.e. each sample).
This track is specified in argument tracks (see
its argument description). By default, a matching row
annotation track is also displayed, but can be disabled
using tracks='basis:'.
a suitable title and
extra information like the fitting algorithm, when
object is a fitted NMF model.
consensusmap redefines default values for the
following arguments of aheatmap:
the colour palette;
the column ordering which is set equal to the row ordering, since a consensus matrix is symmetric;
the distance and linkage methods used to order the rows (and columns). The default is to use 1 minus the consensus matrix itself as distance, and average linkage.
the addition of two
special named annotation tracks, 'basis:' and
'consensus:', that show, for each column (i.e.
each sample), the dominant basis component in the best
fit and the hierarchical clustering of the consensus
matrix respectively (using 1-consensus as distance and
average linkage).
These tracks are specified in argument tracks,
which behaves as in basismap.
a suitable title and extra information like the
type of NMF model or the fitting algorithm, when
object is a fitted NMF model.
signature(object = "NMF"): Plots a
heatmap of the basis matrix of the NMF model
object. This method also works for fitted NMF
models (i.e. NMFfit objects).
signature(object = "NMFfitX"):
Plots a heatmap of the basis matrix of the best fit in
object.
signature(object = "NMF"): The
default method for NMF objects has special default values
for some arguments of aheatmap (see
argument description).
signature(object = "NMFfitX"):
Plots a heatmap of the coefficient matrix of the best fit
in object.
This method adds:
an extra special column
annotation track for multi-run NMF fits,
'consensus:', that shows the consensus cluster
associated to each sample.
a column sorting schema
'consensus' that can be passed to argument
Colv and orders the columns using the hierarchical
clustering of the consensus matrix with average linkage,
as returned by consensushc(object). This is
also the ordering that is used by default for the heatmap
of the consensus matrix as ploted by
consensusmap.
signature(object = "NMFfitX"):
Plots a heatmap of the consensus matrix obtained when
fitting an NMF model with multiple runs.
signature(object = "NMF"):
Plots a heatmap of the connectivity matrix of an NMF
model.
signature(object = "matrix"):
Main method that redefines default values for arguments
of aheatmap.
#---------- # heatmap-NMF #---------- ## More examples are provided in demo `heatmaps` ## Not run: demo(heatmaps) ## End(Not run) ## # random data with underlying NMF model v <- syntheticNMF(20, 3, 10) # estimate a model x <- nmf(v, 3) #---------- # basismap #---------- # show basis matrix basismap(x) ## Not run: # without the default annotation tracks basismap(x, tracks=NA) ## End(Not run) #---------- # coefmap #---------- # coefficient matrix coefmap(x) ## Not run: # without the default annotation tracks coefmap(x, tracks=NA) ## End(Not run) #---------- # consensusmap #---------- ## Not run: res <- nmf(x, 3, nrun=3) consensusmap(res) ## End(Not run)
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