R/jamba-mixedSort.R
mixedSort.Rdsort alphanumeric values keeping numeric values in proper order
mixedSort(
x,
blanksFirst = TRUE,
na.last = NAlast,
keepNegative = FALSE,
keepInfinite = FALSE,
keepDecimal = FALSE,
ignore.case = TRUE,
useCaseTiebreak = TRUE,
honorFactor = FALSE,
sortByName = FALSE,
verbose = FALSE,
NAlast = TRUE,
...
)vector
logical whether to order blank entries before entries
containing a value.
logical indicating whether to move NA entries at
the end of the sort.
logical whether to keep '-' associated with adjacent
numeric values, in order to sort them as negative values.
logical whether to allow "Inf" to be considered
a numeric infinite value.
logical whether to keep the decimal in numbers,
sorting as a true number and not as a version number. By default
keepDecimal=FALSE, which means "v1.200" should be ordered before
"v1.30". When keepDecimal=TRUE, the numeric sort considers only
"1.2" and "1.3" and sorts in that order.
logical whether to ignore uppercase and lowercase
characters when defining the sort order. Note that when x is
factor the factor levels are converted using
unique(toupper(levels(x))), therefore the values in x will be
sorted by factor level.
logical indicating whether to break ties
when ignore.case=TRUE, using mixed case as a tiebreaker.
logical whether to sort the vector x by names(x) instead
of sorting by x itself.
logical whether to print verbose output.
logical deprecated in favor of argument na.last
for consistency with base::sort().
additional parameters are sent to mixedOrder.
vector of values from argument x, ordered by
mixedOrder(). The output class should match class(x).
This function is a refactor of gtools::mixedsort(), a clever bit of
R coding from the gtools package. It was extended to make it slightly
faster, and to handle special cases slightly differently.
It was driven by the need to sort gene symbols, miRNA symbols, chromosome
names, all with proper numeric order, for example:
miR-12,miR-1,miR-122,miR-1b,mir-1a
gtools::mixedsort:miR-122,miR-12,miR-1,miR-1a,mir-1b
mixedSort:miR-1,miR-1a,miR-1b,miR-12,miR-122
The function does not by default recognize negative numbers as negative,
instead it treats '-' as a delimiter, unless keepNegative=TRUE.
This function also attempts to maintain '.' as part of a decimal number, which can be problematic when sorting IP addresses, for example.
This function is really just a wrapper function for mixedOrder(),
which does the work of defining the appropriate order.
The sort logic is roughly as follows:
Split each term into alternating chunks containing character
or numeric substrings, split across columns in a matrix.
Apply appropriate ignore.case logic to the character substrings,
effectively applying toupper() on substrings
Define rank order of character substrings in each matrix column, maintaining ties to be resolved in subsequent columns.
Convert character to numeric ranks via factor intermediate,
defined higher than the highest numeric substring value.
When ignore.case=TRUE and useCaseTiebreak=TRUE, an additional
tiebreaker column is defined using the character substring values
without applying toupper().
A final tiebreaker column is the input string itself, with toupper()
applied when ignore.case=TRUE.
Apply order across all substring columns.
Therefore, some expected behaviors:
When ignore.case=TRUE and useCaseTiebreak=TRUE (default for both)
the input data is ordered without regard to case, then the tiebreaker
applies case-specific sort criteria to the final product. This logic
is very close to default sort() except for the handling of internal
numeric values inside each string.
Other jam sort functions:
mixedOrder(),
mixedSortDF(),
mixedSorts(),
mmixedOrder()
Other jam string functions:
asSize(),
breaksByVector(),
cPasteSU(),
cPasteS(),
cPasteUnique(),
cPasteU(),
cPaste(),
fillBlanks(),
formatInt(),
gsubOrdered(),
gsubs(),
makeNames(),
mixedOrder(),
mixedSortDF(),
mixedSorts(),
mmixedOrder(),
nameVectorN(),
nameVector(),
padInteger(),
padString(),
pasteByRowOrdered(),
pasteByRow(),
sizeAsNum(),
tcount(),
ucfirst(),
uniques()
x <- c("miR-12","miR-1","miR-122","miR-1b", "miR-1a", "miR-2");
sort(x);
#> [1] "miR-1" "miR-12" "miR-122" "miR-1a" "miR-1b" "miR-2"
mixedSort(x);
#> [1] "miR-1" "miR-1a" "miR-1b" "miR-2" "miR-12" "miR-122"
# test honorFactor
mixedSort(factor(c("Cnot9", "Cnot8", "Cnot10")))
#> [1] Cnot8 Cnot9 Cnot10
#> Levels: Cnot10 Cnot8 Cnot9
mixedSort(factor(c("Cnot9", "Cnot8", "Cnot10")), honorFactor=TRUE)
#> [1] Cnot10 Cnot8 Cnot9
#> Levels: Cnot10 Cnot8 Cnot9
# test ignore.case
mixedSort(factor(c("Cnot9", "Cnot8", "CNOT9", "Cnot10")))
#> [1] Cnot8 CNOT9 Cnot9 Cnot10
#> Levels: CNOT9 Cnot10 Cnot8 Cnot9
mixedSort(factor(c("CNOT9", "Cnot8", "Cnot9", "Cnot10")))
#> [1] Cnot8 CNOT9 Cnot9 Cnot10
#> Levels: CNOT9 Cnot10 Cnot8 Cnot9
mixedSort(factor(c("Cnot9", "Cnot8", "CNOT9", "Cnot10")), ignore.case=FALSE)
#> [1] CNOT9 Cnot8 Cnot9 Cnot10
#> Levels: CNOT9 Cnot10 Cnot8 Cnot9
mixedSort(factor(c("Cnot9", "Cnot8", "CNOT9", "Cnot10")), ignore.case=TRUE)
#> [1] Cnot8 CNOT9 Cnot9 Cnot10
#> Levels: CNOT9 Cnot10 Cnot8 Cnot9
mixedSort(factor(c("Cnot9", "Cnot8", "CNOT9", "Cnot10")), useCaseTiebreak=TRUE)
#> [1] Cnot8 CNOT9 Cnot9 Cnot10
#> Levels: CNOT9 Cnot10 Cnot8 Cnot9
mixedSort(factor(c("CNOT9", "Cnot8", "Cnot9", "Cnot10")), useCaseTiebreak=FALSE)
#> [1] Cnot8 CNOT9 Cnot9 Cnot10
#> Levels: CNOT9 Cnot10 Cnot8 Cnot9