Description Usage Arguments Value
transform a matrix (center/scaling; truncation; clustering;) for heatmap; strongly recommends first apply subsetMainMat to get input mat since some attributes are used
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mat |
a matrix, usually from subsetMainMat() |
scale |
selection from c("none", "row", "column") |
clusterWithScaledData |
logical indicating if use scaled data for clustering; default is FALSE |
cluster_rows |
whether to cluster rows |
cluster_cols |
whether to cluster columns |
clustering_distance_rows |
distance metric for rows |
clustering_distance_cols |
distance metric for cols |
clustering_method |
clustering method |
truncate |
logical indicating if truncation is needed; default is NA will enable truncate if scale!='none' |
q1 |
parameter q1 to truncByLimit |
q2 |
parameter q2 to truncByLimit |
Lower |
parameter Lower to truncByQuantile() |
Upper |
parameter Upper to truncByQuantile() |
a matrix with elements gSel, sSel, tree_row, tree_col and so on
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