v1.3.0

Changes:

• plotHeatmap accepts data.frame or ExpressionSet objects for the data argument (calls data.matrix or exprs on object and sends to matrix version)
• Added plotBarplot to plot a barplot for 1 cluster or comparison of 2 clusters along with tests.
• Added whichClusters argument to clusterMatrix to return only clusters corresponding to certain clusters. Mainly relevant for using arguments like workflow that are used by other commands (otherwise could just index the complete matrix manually...)

Bug fixes:

• plotHeatmap now goes through the clusterLegend input and removes levels that do not exist in the sampleData; this was causing incorrect coloring when the clusterLegend had more (or less) levels that it assigned color to than the sampleData did (e.g. if sampleData was a subset of larger dataset upon which the original colors were assigned.) NOTE: that this now has the effect of NOT plotting all values in the clusterLegend if they are not represented in the data, thus changing the previous behavior of plotHeatmap legend.
• fixed bug in how plotHeatmap checked that the dimensions of user-supplied dendrogram match that of data (matrix version).
• fixed convertClusterLegend so when output is matrixNames or matrixColors, the resulting matrix has the colnames equal to cluster labels, like clusterMatrix.