top_rows_heatmap-matrix-method: Heatmap of top rows from different top methods

Description Usage Arguments Details Value Author(s) Examples

Description

Heatmap of top rows from different top methods

Usage

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## S4 method for signature 'matrix'
top_rows_heatmap(object, all_top_value_list = NULL,
    top_value_method = all_top_value_methods(),
    top_n = round(0.25*nrow(object)), layout_nr = 1, 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.

top_n

number of top rows to show.

layout_nr

number of rows in the layout.

scale_rows

whether scale rows.

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, so the heatmaps show which top value method gives better candidate rows for the classification.

Value

No value is returned.

Author(s)

Zuguang Gu <[email protected]>

Examples

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

jokergoo/cola documentation built on Nov. 13, 2018, 1:22 p.m.