Deprecated matrix transformations — matrix

A collection of transformations that operate directly on matrices.

Usage

mtx_rarefy(
  mtx,
  margin = 2L,
  depth = 0.1,
  n = NULL,
  seed = 0L,
  upsample = NULL,
  cpus = NULL
)

mtx_percent(mtx, margin = 2L)

mtx_rescale(mtx, margin = 2L, range = c(0, 1))

rarefy_cols(mtx, depth = 0.1, n = NULL, seed = 0L, cpus = NULL)

rescale_rows(mtx)

rescale_cols(mtx)

Arguments

mtx: A numeric matrix or sparse matrix of counts.
margin: Apply the transformation to the matrix's rows (margin=1L) or columns (margin=2L). Instead of 1L and 2L, you may also use 'rows' and 'cols'. Default: 2L (column-wise, aka sample-wise for otu tables)
depth: How many observations to keep per sample.
n: Deprecated. The number of samples to keep. This argument is ignored in the current version.
seed: An integer seed for randomizing which observations to keep or drop.
upsample: If the count data is in percentages, provide an integer value here to scale each sample's observations to integers that sum to this value before rarefying. See biom_inflate().
cpus: The number of CPUs to use. Set to NULL to use all available, or to 1 to disable parallel processing. Does not affect results. Default: ecodive::n_cpus() (all available cores)
range: When rescaling, what should the minimum and maximum values be? Default: c(0, 1)

Value

A A numeric matrix or sparse matrix, depending on the input type, with the same dimensions as mtx.

Examples

    mtx <- matrix(1:12, ncol = 3, dimnames = list(paste0("OTU", 1:4), paste0("Sample", 1:3)))

    mtx
#>      Sample1 Sample2 Sample3
#> OTU1       1       5       9
#> OTU2       2       6      10
#> OTU3       3       7      11
#> OTU4       4       8      12

    suppressWarnings({

      mtx_rarefy(mtx)

      rarefy_cols(mtx)

      mtx_percent(mtx)

      mtx_rescale(mtx)

      rescale_rows(mtx)

      rescale_cols(mtx)

    })
#>      Sample1   Sample2   Sample3
#> OTU1     0.1 0.1923077 0.2142857
#> OTU2     0.2 0.2307692 0.2380952
#> OTU3     0.3 0.2692308 0.2619048
#> OTU4     0.4 0.3076923 0.2857143