Return a matrix that highlights reverse rank orders of features of interest by column

Source: R/rrank.R

Return a matrix that highlights reverse rank orders of features of interest by column

rrankInd(matrix, ind, inValue = 1L, outValue = 0L, ...)

Arguments

matrix

A matrix

ind

An integer vector or a logical vector that gives the index

inValue

Value to highlight the reverse ranks indexed by ind, see details below

outValue

Values assigned to other values not indexed by ind

...

Passed to rank

Value

A matrix of the same dimension and attributes of the input matrix, each column contains a vector of inValue and outValue. Positions that match the reverse ranks of matrix values indexed by ind are assigned the inValue, otherwise, the outValue.

The function can be used to visualize the reverse ranks of features of interest (rows of the input matrix) in each sample (columns of the input matrix). This is for instance useful for rank plots of features for gene-set enrichment analysis.

Imagine that all features indexed by ind are the larger than all other features in each sample, then the returned matrix will have value 1 in the first rows (the number determined by the features indxed by ind), and 0 in the rest rows.

See also

rank

Examples

testMatrix <- matrix(c(3,6,4,5,2,4,8,3,2,5,4,7), ncol=3, byrow=FALSE)
print(testMatrix)
#>      [,1] [,2] [,3]
#> [1,]    3    2    2
#> [2,]    6    4    5
#> [3,]    4    8    4
#> [4,]    5    3    7
testInd <- c(2,4)
## verify that the command below returns 1 in positions occupied by 
## the reverse ranks of the values indexed by testInd
rrankInd(testMatrix, testInd)
#>      [,1] [,2] [,3]
#> [1,]    1    0    1
#> [2,]    1    1    1
#> [3,]    0    1    0
#> [4,]    0    0    0
testIndBool <- c(FALSE, TRUE, FALSE, TRUE)
rrankInd(testMatrix, testIndBool)
#>      [,1] [,2] [,3]
#> [1,]    1    0    1
#> [2,]    1    1    1
#> [3,]    0    1    0
#> [4,]    0    0    0