clust_cormap: Cluster a correlation matrix and return the sorted matrix for...
In coreheat: Correlation Heatmaps

Description Usage Arguments Value

View source: R/cormap2.R

Helper function to cluster the correlation matrix and return the sorted matrix for plotting.

clust_cormap(
  cormat,
  na.frac = 0.1,
  distfn = function(cm) (1 - cm),
  method = "complete",
  cor.cluster = 1,
  cor.window = NULL,
  cor.thr = 0.8,
  cor.mar = 0.05,
  cut.thr = 0.9,
  cut.size = 5,
  list.output = FALSE,
  verbose = FALSE
)

`cormat`	(`numeric` or `list`). The correlation matrix or a list containing matrices of correlation values and P-Values as generated by `eset_cor`. If a list then the correlation matrix is expected to be in slot 'cor' and the matrix of P-Values in slot 'pvalues'.
`na.frac`	(`numeric`). Fraction of missing values allowed per row of the input matrix. Defaults to `0.1` which means LESS than 10per centof the values in one row are allowed to be NAs.
`distfn`	(`function`). Function to calculate the dissimilarity matrix for clustering. Defaults to `function(cm) (1-cm)`.
`method`	(`character`). The agglomeration method used for clustering. See help for `hclust`. Defaults to "complete".
`cor.cluster`	(`numeric`). The correlation cluster along the diagonal 'line' in the heatmap that should be zoomed into. A sliding window of size `cor.window` will be moved along the diagonal of the correlation matrix to find the cluster with the most corelation values meeting `core.thr`. Defaults to `1`.
`cor.window`	(`numeric`). The size of the sliding window (see `cor.cluster`). Defaults to `NULL`. Note that this works only for positive correlations.
`cor.thr`	(`numeric`). Correlation threshold to filter the correlation matrix for plotting. Defaults to `NULL` meaning no filtering. See also cor.mar. This value is sign-sensitive: a negative threshold will retain rows and columns of the correlation matrix with correlation values between -1 and the threshold, a positive value will retain rows and columns with values between the threshold and 1. Zero (0) is treated as positive.
`cor.mar`	(`numeric`). Margin of the values per row of the correlation matrix the cor.thr filter needs to meet. Defaults to `0.5` meaning at least 50 per cent of the values in a row need to meet the threshold in order to keep the row.
`cut.thr`	(`numeric`). Threshold at which dendrogram branches are to be cut. Passed on to argument `cutHeight` in `cutreeStatic`. Defaults to `NULL` meaning no cutting.
`cut.size`	(`numeric`). Minimum number of objects on a dendrogram branch considered a cluster. Passed on to argument `minSize` in `cutreeStatic`. Defaults to `5`.
`list.output`	(`logical`). Should the output be a list of different object created in the call? Depends also on input type. If `FALSE` only the (filtered) correlation matrix is returned.
`verbose`	(`logical`). Should verbose output be written to the console? Defaults to `FALSE`.