Heatmap of top rows from different top-value methods

# S4 method for matrix
top_rows_heatmap(object, all_top_value_list = NULL,
    top_value_method = all_top_value_methods(),
    bottom_annotation = NULL,
    top_n = round(0.25*nrow(object)), scale_rows = TRUE, ...)

Arguments

object: A numeric matrix.
all_top_value_list: Top-values that have already been calculated from the matrix. If it is NULL the values are calculated by methods in top_value_method argument.
top_value_method: Methods defined in all_top_value_methods.
bottom_annotation: A HeatmapAnnotation-class object.
top_n: Number of top rows to show in the heatmap.
scale_rows: Whether to scale rows.
...: Pass to Heatmap.

Details

The function makes heatmaps where the rows are scaled (or not scaled) for the top n rows from different top-value methods.

The top n rows are used for subgroup classification in cola analysis, so the heatmaps show which top-value method gives better candidate rows for the classification.

Value

No value is returned.

Author

Zuguang Gu <z.gu@dkfz.de>

Examples

set.seed(123)
mat = matrix(rnorm(1000), nrow = 100)
top_rows_heatmap(mat, top_n = 25)