sort data.frame keeping numeric values in proper order
data.frame input
one of two types of input:
integer vector referring to the order of columns to be
used by mmixedOrder() to order the data.frame. Note that
negative values will reverse the sort order for the corresponding
column number. To sort rownames(df) use zero 0, and to reverse
sorting rownames(x) use -0.1 where the negative sign will
reverse the sort, and -0.1 will be rounded to 0.
character vector of values in colnames(df),
optionally including prefix "-" to reverse the sort.
Note that the argument decreasing can also be used to specify
columns to have reverse sort, either as a single value or vector
to be applied to each column in byCols. To sort rownames(df)
use "rownames" or "row.names". To reverse sorting rownames(df)
use "-rownames" or "-row.names".
logical whether to move NA entries to the end of the sort.
When na.last=TRUE then NA values will always be last, even following
blanks and infinite values. When na.last=FALSE then NA values
will always be first, even before blanks and negative infinite values.
NULL or logical vector indicating which columns
in byCols should be sorted in decreasing order. By default, the
sign(byCols) is used to define the sort order of each column, but it
can be explicitly overridden with this decreasing parameter.
logical whether to use rownames(df) as a last
tiebreaker in the overall rank ordering. This parameter has the primary
effect of assuring a reproducible result, provided the rownames are
consistently defined, or if rownames are actually row numbers.
When useRownames=FALSE then rows that would otherwise be ties
will be returned in the same order they were provided in df.
logical whether to print verbose output. When
verbose=2 there is slightly more verbose output.
arguments passed to mmixedOrder(), except sortByName which is not
passed along.
additional arguments passed to mmixedOrder() for custom
sort options as described in mixedSort().
data.frame whose rows are ordered using mmixedOrder().
This function is a wrapper around mmixedOrder() so it operates
on data.frame columns in the proper order, using logic similar that used
by base::order() when operating on a data.frame. The sort order logic
is fully described in mixedSort() and mixedOrder().
Note that byCols can either be given as integer column index values,
or character vector of colnames(x). In either case, using negative
prefix - will reverse the sort order of the corresponding column.
For example byCols=c(2, -1) will sort column 2 increasing, then
column 1 decreasing.
Similarly, one can supply colnames(df), such as
byCols=c("colname2", "-colname1"). Values are matched as-is to
colnames(df) first, then any values not matched are compared again
after removing prefix - from the start of each character string.
Therefore, if colnames(df) contains "-colname1" it will be matched
as-is, but "--colname1" will only be matched after removing the first -,
after which the sort order will be reversed for that column.
For direct control over the sort order of each column defined in byCols,
you can supply logical vector to argument decreasing, and this vector
is recycled to length(byCols).
Finally, for slight efficiency, only unique columns defined in byCols
are used to determine the row order, so even if a column is defined twice
in byCols, only the first instance is passed to mmixedOrder() to
determine row order.
Other jam sort functions:
mixedOrder(),
mixedSorts(),
mixedSort(),
mmixedOrder()
Other jam string functions:
asSize(),
breaksByVector(),
cPasteSU(),
cPasteS(),
cPasteUnique(),
cPasteU(),
cPaste(),
fillBlanks(),
formatInt(),
gsubOrdered(),
gsubs(),
makeNames(),
mixedOrder(),
mixedSorts(),
mixedSort(),
mmixedOrder(),
nameVectorN(),
nameVector(),
padInteger(),
padString(),
pasteByRowOrdered(),
pasteByRow(),
sizeAsNum(),
tcount(),
ucfirst(),
uniques()
# start with a vector of miRNA names
x <- c("miR-12","miR-1","miR-122","miR-1b", "miR-1a","miR-2");
# add some arbitrary group information
g <- rep(c("Air", "Treatment", "Control"), 2);
# create a data.frame
df <- data.frame(group=g,
miRNA=x,
stringsAsFactors=FALSE);
# input data
df;
#> group miRNA
#> 1 Air miR-12
#> 2 Treatment miR-1
#> 3 Control miR-122
#> 4 Air miR-1b
#> 5 Treatment miR-1a
#> 6 Control miR-2
# output when using order()
df[do.call(order, df), , drop=FALSE];
#> group miRNA
#> 1 Air miR-12
#> 4 Air miR-1b
#> 3 Control miR-122
#> 6 Control miR-2
#> 2 Treatment miR-1
#> 5 Treatment miR-1a
# output with mixedSortDF()
mixedSortDF(df);
#> Warning: 'length(x) = 2 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 2 > 1' in coercion to 'logical(1)'
#> group miRNA
#> 4 Air miR-1b
#> 1 Air miR-12
#> 6 Control miR-2
#> 3 Control miR-122
#> 2 Treatment miR-1
#> 5 Treatment miR-1a
# mixedSort respects factor order
# reorder factor levels to demonstrate.
# "Control" should come first
gf <- factor(g, levels=c("Control", "Air", "Treatment"));
df2 <- data.frame(groupfactor=gf,
miRNA=x,
stringsAsFactors=FALSE);
# now the sort properly keeps the group factor levels in order,
# which also sorting the miRNA names in their proper order.
mixedSortDF(df2);
#> Warning: 'length(x) = 2 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 2 > 1' in coercion to 'logical(1)'
#> groupfactor miRNA
#> 6 Control miR-2
#> 3 Control miR-122
#> 4 Air miR-1b
#> 1 Air miR-12
#> 2 Treatment miR-1
#> 5 Treatment miR-1a
x <- data.frame(l1=letters[1:10],
l2=rep(letters[1:2+10], 5),
L1=LETTERS[1:10],
L2=rep(LETTERS[1:2+20], each=5));
set.seed(123);
rownames(x) <- sample(seq_len(10));
x;
#> l1 l2 L1 L2
#> 3 a k A U
#> 10 b l B U
#> 2 c k C U
#> 8 d l D U
#> 6 e k E U
#> 9 f l F V
#> 1 g k G V
#> 7 h l H V
#> 5 i k I V
#> 4 j l J V
# sort by including rownames
mixedSortDF(x, byCols=c("rownames"));
#> Warning: 'length(x) = 2 > 1' in coercion to 'logical(1)'
#> l1 l2 L1 L2
#> 1 g k G V
#> 2 c k C U
#> 3 a k A U
#> 4 j l J V
#> 5 i k I V
#> 6 e k E U
#> 7 h l H V
#> 8 d l D U
#> 9 f l F V
#> 10 b l B U
mixedSortDF(x, byCols=c("L2", "-rownames"));
#> Warning: 'length(x) = 2 > 1' in coercion to 'logical(1)'
#> Warning: 'length(x) = 2 > 1' in coercion to 'logical(1)'
#> l1 l2 L1 L2
#> 10 b l B U
#> 8 d l D U
#> 6 e k E U
#> 3 a k A U
#> 2 c k C U
#> 9 f l F V
#> 7 h l H V
#> 5 i k I V
#> 4 j l J V
#> 1 g k G V
# demonstrate sorting a matrix with no rownames
m <- matrix(c(2, 1, 3, 4), ncol=2);
mixedSortDF(m, byCols=-2)
#> [,1] [,2]
#> [1,] 1 4
#> [2,] 2 3
# add rownames
rownames(m) <- c("c", "a");
mixedSortDF(m, byCols=0)
#> Warning: 'length(x) = 2 > 1' in coercion to 'logical(1)'
#> [,1] [,2]
#> a 1 4
#> c 2 3
mixedSortDF(m, byCols="-rownames")
#> Warning: 'length(x) = 2 > 1' in coercion to 'logical(1)'
#> [,1] [,2]
#> c 2 3
#> a 1 4
mixedSortDF(m, byCols="rownames")
#> Warning: 'length(x) = 2 > 1' in coercion to 'logical(1)'
#> [,1] [,2]
#> a 1 4
#> c 2 3
mixedSortDF(data.frame(factor1=factor(c("Cnot9", "Cnot8", "Cnot10"))), honorFactor=FALSE)
#> Warning: 'length(x) = 2 > 1' in coercion to 'logical(1)'
#> factor1
#> 2 Cnot8
#> 1 Cnot9
#> 3 Cnot10
# test date columns
testfiles <- system.file(package="jamba", c("TODO.md", "README.md", "NEWS.md"))
testinfo <- file.info(testfiles)
testinfo
#> size
#> /private/var/folders/1v/hbvdjhy1293cvqlm7n6l_hxw0000gs/T/Rtmphg9J6i/temp_libpathf97849a49351/jamba/NEWS.md 106174
#> isdir
#> /private/var/folders/1v/hbvdjhy1293cvqlm7n6l_hxw0000gs/T/Rtmphg9J6i/temp_libpathf97849a49351/jamba/NEWS.md FALSE
#> mode
#> /private/var/folders/1v/hbvdjhy1293cvqlm7n6l_hxw0000gs/T/Rtmphg9J6i/temp_libpathf97849a49351/jamba/NEWS.md 644
#> mtime
#> /private/var/folders/1v/hbvdjhy1293cvqlm7n6l_hxw0000gs/T/Rtmphg9J6i/temp_libpathf97849a49351/jamba/NEWS.md 2024-06-10 13:42:47
#> ctime
#> /private/var/folders/1v/hbvdjhy1293cvqlm7n6l_hxw0000gs/T/Rtmphg9J6i/temp_libpathf97849a49351/jamba/NEWS.md 2024-06-10 13:42:50
#> atime
#> /private/var/folders/1v/hbvdjhy1293cvqlm7n6l_hxw0000gs/T/Rtmphg9J6i/temp_libpathf97849a49351/jamba/NEWS.md 2024-06-10 13:42:47
#> uid
#> /private/var/folders/1v/hbvdjhy1293cvqlm7n6l_hxw0000gs/T/Rtmphg9J6i/temp_libpathf97849a49351/jamba/NEWS.md 505
#> gid
#> /private/var/folders/1v/hbvdjhy1293cvqlm7n6l_hxw0000gs/T/Rtmphg9J6i/temp_libpathf97849a49351/jamba/NEWS.md 20
#> uname
#> /private/var/folders/1v/hbvdjhy1293cvqlm7n6l_hxw0000gs/T/Rtmphg9J6i/temp_libpathf97849a49351/jamba/NEWS.md wardjm
#> grname
#> /private/var/folders/1v/hbvdjhy1293cvqlm7n6l_hxw0000gs/T/Rtmphg9J6i/temp_libpathf97849a49351/jamba/NEWS.md staff
mixedSortDF(testinfo, byCols="mtime")
#> size
#> /private/var/folders/1v/hbvdjhy1293cvqlm7n6l_hxw0000gs/T/Rtmphg9J6i/temp_libpathf97849a49351/jamba/NEWS.md 106174
#> isdir
#> /private/var/folders/1v/hbvdjhy1293cvqlm7n6l_hxw0000gs/T/Rtmphg9J6i/temp_libpathf97849a49351/jamba/NEWS.md FALSE
#> mode
#> /private/var/folders/1v/hbvdjhy1293cvqlm7n6l_hxw0000gs/T/Rtmphg9J6i/temp_libpathf97849a49351/jamba/NEWS.md 644
#> mtime
#> /private/var/folders/1v/hbvdjhy1293cvqlm7n6l_hxw0000gs/T/Rtmphg9J6i/temp_libpathf97849a49351/jamba/NEWS.md 2024-06-10 13:42:47
#> ctime
#> /private/var/folders/1v/hbvdjhy1293cvqlm7n6l_hxw0000gs/T/Rtmphg9J6i/temp_libpathf97849a49351/jamba/NEWS.md 2024-06-10 13:42:50
#> atime
#> /private/var/folders/1v/hbvdjhy1293cvqlm7n6l_hxw0000gs/T/Rtmphg9J6i/temp_libpathf97849a49351/jamba/NEWS.md 2024-06-10 13:42:47
#> uid
#> /private/var/folders/1v/hbvdjhy1293cvqlm7n6l_hxw0000gs/T/Rtmphg9J6i/temp_libpathf97849a49351/jamba/NEWS.md 505
#> gid
#> /private/var/folders/1v/hbvdjhy1293cvqlm7n6l_hxw0000gs/T/Rtmphg9J6i/temp_libpathf97849a49351/jamba/NEWS.md 20
#> uname
#> /private/var/folders/1v/hbvdjhy1293cvqlm7n6l_hxw0000gs/T/Rtmphg9J6i/temp_libpathf97849a49351/jamba/NEWS.md wardjm
#> grname
#> /private/var/folders/1v/hbvdjhy1293cvqlm7n6l_hxw0000gs/T/Rtmphg9J6i/temp_libpathf97849a49351/jamba/NEWS.md staff