annHeatmap2: Annotated heatmaps
In Heatplus: Heatmaps with row and/or column covariates and colored clusters

Description Usage Arguments Details Value See Also Examples

This function plots a data matrix as intensity heatmap, with optional dendrograms, annotation panels and clustering for both rows and columns. This is the actual working function called by numerous wrappers.

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annHeatmap2(x, dendrogram, annotation, cluster, labels, 
            scale = c("row", "col", "none"), breaks=256, col = g2r.colors,
            legend = FALSE)

`x`	the numerical matrix to be shown as heatmap
`dendrogram`	a list that controls how row- and column diagrams are determined and displayed
`annotation`	a list that controls the data and the way it is shown in row- and column annotation panels
`cluster`	a list that controls how many clusters are chosen, and how these clusters are labelled and colored
`labels`	a list that controls the row- and column labels, as well as their size and placement
`scale`	a character string indicating how the matrix `x` is standardized (by row, by column or not at all). This affects only display, not dendrograms or clustering
`breaks`	specifies the interval breaks for displaying the data in `x`; either a vector of explicit interval breaks, or just the desired number of intervals. See `niceBreaks` for details.
`col`	specifies a palette of colors for the heatmap intensities; either a vector of explicit color definitions (one less than breaks) or a palette function. See `breakColors`.
`legend`	whether and where to draw a legend for the colors/intervals in the heatmap. If `TRUE`, a legend is placed in a position determined by the function to be suitable; alternatively, integer values 1-4 indicate the side where the legend is to be drawn; and `FALSE` indicates that no legend should be drawn.

Arguments scale, breaks, col and legend control different aspects of the whole plot directly as described. Arguments dendrogram, annotation, cluster and labels control aspects that may differ for the rows and columns of the central heatmap and have a special structure: each is a named list with different entries controling e.g. the look of a dendrogram, the data for annotation etc. Additionally, they can contain two extra entries called simply Row and Col; these are again named lists that can contain all the same entries as the parent list. Entries specified directly in the list apply to both rows and columns; entries specified as part of Row or Col override these defaults for the rows or columns only.

Recognized parameters for argument dendrogram:

clustfun: the clustering function for generating the dendrogram; defaults to hclust for rows and columns
distfun: a function that returns the pairwise distances between samples/features as an object of class dist; defaults to dist for rows and columns
status: a string that controls the display of the dendrogram: yes means use the dendrogram to re-order the rows/columns and display the dendrogram; hidden means re-rorder, but do not display; no means do not use the dendrogram at all.
lwd: the line width of the branches of the dendrogram; defaults to 3.
dendro: an override argument that allows to pass in a dendrogram directly, bypassing the clustfun and distfun mechanism; defaults to NULL (i.e. is not used)

Recognized entries for argument annotation:

data: a data frame containing the annotation data; defaults to NULL, i.e. no annotation is displayed
control: a list of fine-tuning parameters that is passed directly to picketPlot; defaults to an empty list, i.e. the default settings in picketPlot
asIs: logical value indicating whether the annotation data needs to be pre-processed via convAnnData or not; defaults to TRUE
inclRef: logical value indicating whether to include all levels of factor variables in data, or whether to drop the reference level (i.e. the first level). Defaults to TRUE

Recognized entries for argument cluster:

cuth: the height at which to cut through the dendrogram to define groups of similar features/samples; defaults to NULL, i.e. no cutting
label: labels for the clusters; defaults to NULL, i.e. no labels
col: colors for the different clusters; the colors are used for coloring both the sub-trees of the dendrogram and the corresponding area in the annotation plot (if there is one). This is either a vector of colors, or a palette function that takes a number and returns a vector of colors of the specified length; defaults to RainbowPastel
grp: an override argument that directly specifies group memberships for the features/samples, completely bypassing the whole dendrogram and cuth mechanism. This probably only works for dendrogram$status="no".

Recognized entries for argument labels:

cex: size of the text for the labels; defaults to NULL, i.e. use a hard-coded default guess
nrow: amount of space available for the labels between the central heatmap and the dendrogram, expressed as lines of text; defaults to 3.
side: side at which to draw the labels, coded as integer between 1 and 4 in the usual way (1 = below the plot, continuing clockwise). A common default for rows and columns does not make sense: rows only work with 2 and 4, columns only with 1 and 3. Defaults try to make use of empty space, depending on the presence of a dendrogram.
labels: labels for rows and columns; defaults to NULL, i.e. using the row- and column names of x. Note that these labels are applied after re-sorting rows and columns as per dendrogram, so these have to be already sorted accordingly. If you want to change the labels before re-sorting, it is is easier to re-set the row- and/or column names of x.

An object of class annHeatmap. Use plot to display it graphically.

heatmapLayout, niceBreaks, breakColors, g2r.colors

require(Biobase)
data(sample.ExpressionSet)
ex1 = sample.ExpressionSet[51:85,]
map1 = annHeatmap2(exprs(ex1), ann=list(Col=list(data=pData(ex1))),
                   cluster=list(Col=list(cuth=3000)))
plot(map1)

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

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