banbh banbh - 3 months ago 12
R Question

How to pad a matrix with named rows and columns?

Suppose you have a matrix (

X
) and a second matrix (
src
) such that rownames of
X
are a subset of the rownames of
src
and the colnames of
X
are a subset of the colnames of
src
. What is the best way to create a matrix with the rows and columns of
src
, the data of
X
, and with missing data filled in with some default value (such as zero or
NA
)?

Below is my attempt, but I feel there must be a standard way of doing this in R.

# Assume row and columns are named
PadColumns <- function(x, src, fill = NA) {
# pad columns with default values
result <- matrix(fill, nrow = nrow(x), ncol = ncol(src))
colnames(result) <- colnames(src)
rownames(result) <- rownames(x)
result[,match(colnames(x), colnames(src))] <- x
result
}

PadRows <- function(x, src, fill = NA) {
# pad rows with default values
result <- matrix(fill, nrow = nrow(src), ncol = ncol(x))
colnames(result) <- colnames(x)
rownames(result) <- rownames(src)
result[match(rownames(x), rownames(src)),] <- x
result
}

PadRowsColumns <- function(x, src, fill = NA) {
PadColumns(PadRows(x, src, fill = fill), src, fill = fill)
}


For example, given

X <- matrix(1:6, nrow = 2, dimnames = list(letters[2 * 1:2], LETTERS[2 * 1:3]))
src <- matrix(0, nrow = 4, ncol = 6, dimnames = list(letters[1:4], LETTERS[1:6]))


then we should get this:

> X
B D F
b 1 3 5
d 2 4 6
> PadRowsColumns(X, src)
A B C D E F
a NA NA NA NA NA NA
b NA 1 NA 3 NA 5
c NA NA NA NA NA NA
d NA 2 NA 4 NA 6

Answer

You can subset matrices by row and column names.

src <- matrix(1, nrow = 3, ncol = 4, 
              dimnames= list(c("a", "b", "c"), c("A", "B", "C", "D")))
X <- matrix(1:6, nrow = 2, ncol = 3,
            dimnames = list(c("b", "c"), c("A", "C", "D")))
Y <- src
Y[] <- NA
Y[rownames(X), colnames(X)] <- X