Make a matrix from a data frame containing species data.
Usage
makeMatrix(
DF,
column,
defaultDiagonal = 100,
defaultValue = NA,
impute = c("no", "average", "missForest", "missForest2"),
...
)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
Method to impute missing value. Defaults to
no.- ...
Other arguments passed to the imputing function.
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.
Note
In case of missing values, the following options are available.
Leave them missing (
NA). This is the default.Give them a fixed value defined by the
devaultValueoption.Impute them from the replicate (when target and query roles are exchanged) if available (
impute=average), else give them the default value.Impute them from the replicate, and then with random forests (
impute=missForest). Hide the diagonal values (which are extreme) when (impute=missForest2).
Examples
df <- Halo_DF
makeMatrix(df, "percent_difference_global", 0, 50)
#> Halobacterium_litoreum Halobacterium_noricense
#> Halobacterium_litoreum 0.00000 21.18801
#> Halobacterium_noricense 21.26064 0.00000
#> 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 0.00000 32.99448
#> Haloferax_mediterranei 33.02111 0.00000
#> 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 0.00000 30.20358
#> Salarchaeum_japonicum 30.17554 0.00000
#> attr(,"builtWith")
#> [1] "percent_difference_global"
# Missing values get NA by default unless specified in the 4th argument.
df["Salarchaeum_japonicum___Haloferax_volcanii", "percent_difference_global"] <- NA
makeMatrix(df, "percent_difference_global", 0)
#> Halobacterium_litoreum Halobacterium_noricense
#> Halobacterium_litoreum 0.00000 21.18801
#> Halobacterium_noricense 21.26064 0.00000
#> 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 0.00000 32.99448
#> Haloferax_mediterranei 33.02111 0.00000
#> 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 0.00000 30.20358
#> Salarchaeum_japonicum NA 0.00000
#> attr(,"builtWith")
#> [1] "percent_difference_global"
makeMatrix(df, "percent_difference_global", 0, impute = "average")
#> Halobacterium_litoreum Halobacterium_noricense
#> Halobacterium_litoreum 0.00000 21.18801
#> Halobacterium_noricense 21.26064 0.00000
#> 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 0.00000 32.99448
#> Haloferax_mediterranei 33.02111 0.00000
#> 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 0.00000 30.20358
#> Salarchaeum_japonicum 30.20358 0.00000
#> attr(,"builtWith")
#> [1] "percent_difference_global"
# NA value imputation with missForest use random numbers
set.seed(1664)
df["Haloferax_volcanii___Salarchaeum_japonicum", "percent_difference_global"] <- NA
makeMatrix(df, "percent_difference_global", 0, impute = "average")
#> Halobacterium_litoreum Halobacterium_noricense
#> Halobacterium_litoreum 0.00000 21.18801
#> Halobacterium_noricense 21.26064 0.00000
#> 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 0.00000 32.99448
#> Haloferax_mediterranei 33.02111 0.00000
#> 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 0.00000 NA
#> Salarchaeum_japonicum NA 0.00000
#> attr(,"builtWith")
#> [1] "percent_difference_global"
makeMatrix(df, "percent_difference_global", 0, impute = "missForest")
#> Halobacterium_litoreum Halobacterium_noricense
#> Halobacterium_litoreum 0.00000 21.18801
#> Halobacterium_noricense 21.26064 0.00000
#> 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 0.00000 32.99448
#> Haloferax_mediterranei 33.02111 0.00000
#> 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 0.00000 14.80374
#> Salarchaeum_japonicum 16.14705 0.00000
#> attr(,"builtWith")
#> [1] "percent_difference_global"
makeMatrix(df, "percent_difference_global", 0, impute = "missForest2")
#> Halobacterium_litoreum Halobacterium_noricense
#> Halobacterium_litoreum 0.00000 21.18801
#> Halobacterium_noricense 21.26064 0.00000
#> 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 0.00000 32.99448
#> Haloferax_mediterranei 33.02111 0.00000
#> 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 0.00000 30.34589
#> Salarchaeum_japonicum 30.44139 0.00000
#> attr(,"builtWith")
#> [1] "percent_difference_global"