Pairwise comparison matrix

Make a matrix from a data frame containing species data.

Usage

makeMatrix(
  DF,
  column,
  defaultDiagonal = 100,
  defaultValue = NA,
  impute = FALSE
)

Arguments

DF

Data frame containing species information, produced with formatStats()

column

The variable from the data frame to extract species data from.

defaultDiagonal

Maximum possible value of variable.

defaultValue

Minimum possible value of variable.

impute

Logical. If TRUE, applies missForest to fill in missing values.

Value

A square matrix where rows and columns are sample identifiers and values are statistics for the pairs of samples. In addition it has an attribute "builtWith" that records the value of column.

Author

Noa Brenner

Charles Plessy

Anika Mittal

Examples

makeMatrix(Halo_DF, "percent_difference_global", 100, 50)
#>                         Halobacterium_litoreum Halobacterium_noricense
#> Halobacterium_litoreum               100.00000                21.18801
#> Halobacterium_noricense               21.26064               100.00000
#> Halobacterium_salinarum               24.15702                25.05241
#> Haloferax_mediterranei                31.72595                33.57159
#> Haloferax_volcanii                    29.88642                30.06817
#> Salarchaeum_japonicum                 27.24648                27.88932
#>                         Halobacterium_salinarum Haloferax_mediterranei
#> Halobacterium_litoreum                 24.24792               31.27923
#> Halobacterium_noricense                25.05377               31.54667
#> Halobacterium_salinarum               100.00000               32.99448
#> Haloferax_mediterranei                 33.02111              100.00000
#> Haloferax_volcanii                     31.51689               19.60559
#> Salarchaeum_japonicum                  28.19145               31.34071
#>                         Haloferax_volcanii Salarchaeum_japonicum
#> Halobacterium_litoreum            29.83707              27.25050
#> Halobacterium_noricense           30.03853              27.57799
#> Halobacterium_salinarum           31.51122              28.44185
#> Haloferax_mediterranei            19.77441              31.58067
#> Haloferax_volcanii               100.00000              30.20358
#> Salarchaeum_japonicum             30.17554             100.00000
#> attr(,"builtWith")
#> [1] "percent_difference_global"

# Missing values get NA by default unless specified in the 4th argument.
makeMatrix(Halo_DF |> tail(-1), "percent_difference_global", 100)
#>                         Halobacterium_litoreum Halobacterium_noricense
#> Halobacterium_litoreum               100.00000                21.26064
#> Halobacterium_noricense               21.26064               100.00000
#> Halobacterium_salinarum               24.15702                25.05241
#> Haloferax_mediterranei                31.72595                33.57159
#> Haloferax_volcanii                    29.88642                30.06817
#> Salarchaeum_japonicum                 27.24648                27.88932
#>                         Halobacterium_salinarum Haloferax_mediterranei
#> Halobacterium_litoreum                 24.24792               31.27923
#> Halobacterium_noricense                25.05377               31.54667
#> Halobacterium_salinarum               100.00000               32.99448
#> Haloferax_mediterranei                 33.02111              100.00000
#> Haloferax_volcanii                     31.51689               19.60559
#> Salarchaeum_japonicum                  28.19145               31.34071
#>                         Haloferax_volcanii Salarchaeum_japonicum
#> Halobacterium_litoreum            29.83707              27.25050
#> Halobacterium_noricense           30.03853              27.57799
#> Halobacterium_salinarum           31.51122              28.44185
#> Haloferax_mediterranei            19.77441              31.58067
#> Haloferax_volcanii               100.00000              30.20358
#> Salarchaeum_japonicum             30.17554             100.00000
#> attr(,"builtWith")
#> [1] "percent_difference_global"