Assign rank to each row in a group in R
0
I have the following input dataframe and would like to first group it by Gene and then arrange by descending Expression. Once I've done that, I'd like to add a Rank column that ranks each row per Gene according to the Expression value - so rows with higher Expression per gene get ranked higher.
I've already done the group by and arrange by part (below), but I'm struggling with how to do the ranking.
dat_sorted <- dat %>% select(Gene, Expression, Sample) %>%
group_by(Gene) %>%
arrange(Gene, desc(Expression))
**INPUT (dat)**
Gene Expression Sample
ENSG00000000027 2.79336700 HSB431
ENSG00000000938 0.83478860 HSB414
ENSG00000000003 2.40009100 HSB618
ENSG00000000938 1.75148448 HSB671
ENSG00000000938 1.52182467 HSB670
ENSG00000000938 0.62174432 HSB459
ENSG00000000003 2.81561500 HSB671
**EXPECTED OUTPUT**
Gene Expression Sample Rank
ENSG00000000003 2.81561500 HSB671 1
ENSG00000000003 2.79336700 HSB431 2
ENSG00000000027 2.79336700 HSB431 1
ENSG00000000938 1.75148448 HSB671 1
ENSG00000000938 1.52182467 HSB670 2
ENSG00000000938 0.83478860 HSB414 3
ENSG00000000938 0.62174432 HSB459 4
UPDATE
When trying:
dat %>%
group_by(Gene) %>%
mutate(Rank = dense_rank(Expression)) %>%
arrange(Gene, Expression, Rank)
I get:
Gene Sample Expression Rank
ENSG00000000003 HSB626 3.52200400 31107
ENSG00000000938 HSB152 -1.60663921 1585
ENSG00000000938 HSB425 -0.40209856 3536
ENSG00000000938 HSB627 -1.09598712 2244
ENSG00000000938 HSB645 -0.82846242 2666
ENSG00000000971 HSB154 4.61434903 53421
ENSG00000000971 HSB154 4.61434903 53421
ENSG00000000971 HSB154 4.61434903 53421
ENSG00000000971 HSB195 2.45561878 18041
ENSG00000000971 HSB222 5.54389646 79697
r dataframe ranking
asked Nov 28 '18 at 17:04
claudiadastclaudiadast
13711
add a comment |
0
I have the following input dataframe and would like to first group it by Gene and then arrange by descending Expression. Once I've done that, I'd like to add a Rank column that ranks each row per Gene according to the Expression value - so rows with higher Expression per gene get ranked higher.
I've already done the group by and arrange by part (below), but I'm struggling with how to do the ranking.
dat_sorted <- dat %>% select(Gene, Expression, Sample) %>%
group_by(Gene) %>%
arrange(Gene, desc(Expression))
**INPUT (dat)**
Gene Expression Sample
ENSG00000000027 2.79336700 HSB431
ENSG00000000938 0.83478860 HSB414
ENSG00000000003 2.40009100 HSB618
ENSG00000000938 1.75148448 HSB671
ENSG00000000938 1.52182467 HSB670
ENSG00000000938 0.62174432 HSB459
ENSG00000000003 2.81561500 HSB671
**EXPECTED OUTPUT**
Gene Expression Sample Rank
ENSG00000000003 2.81561500 HSB671 1
ENSG00000000003 2.79336700 HSB431 2
ENSG00000000027 2.79336700 HSB431 1
ENSG00000000938 1.75148448 HSB671 1
ENSG00000000938 1.52182467 HSB670 2
ENSG00000000938 0.83478860 HSB414 3
ENSG00000000938 0.62174432 HSB459 4
UPDATE
When trying:
dat %>%
group_by(Gene) %>%
mutate(Rank = dense_rank(Expression)) %>%
arrange(Gene, Expression, Rank)
I get:
Gene Sample Expression Rank
ENSG00000000003 HSB626 3.52200400 31107
ENSG00000000938 HSB152 -1.60663921 1585
ENSG00000000938 HSB425 -0.40209856 3536
ENSG00000000938 HSB627 -1.09598712 2244
ENSG00000000938 HSB645 -0.82846242 2666
ENSG00000000971 HSB154 4.61434903 53421
ENSG00000000971 HSB154 4.61434903 53421
ENSG00000000971 HSB154 4.61434903 53421
ENSG00000000971 HSB195 2.45561878 18041
ENSG00000000971 HSB222 5.54389646 79697
r dataframe ranking
asked Nov 28 '18 at 17:04
claudiadastclaudiadast
13711
2
... %>% mutate(Rank = 1:n()), this relies on yourarrangeordering. Or using therankfunction (which ranks low to high, so we need a negative)... %>% mutate(Rank = rank(-Expression)), which just uses theExpressionvalues so it doesn't depend on the ordering. Alsorankhas several options for dealing with ties.
– Gregor
Nov 28 '18 at 17:07
@Gregor: Do you mind providing a complete example? I've tried variations of what you suggested but am still not having any luck.
– claudiadast
Nov 28 '18 at 17:32
2
From your edit it looks like you've loadedplyrafterdplyrand ignored the warnings. See this R-FAQ. Rundetach(package:plyr)or specifydplyr::mutateand it should work.
– Gregor
Nov 28 '18 at 17:34
add a comment |
0
0
0
I have the following input dataframe and would like to first group it by Gene and then arrange by descending Expression. Once I've done that, I'd like to add a Rank column that ranks each row per Gene according to the Expression value - so rows with higher Expression per gene get ranked higher.
I've already done the group by and arrange by part (below), but I'm struggling with how to do the ranking.
dat_sorted <- dat %>% select(Gene, Expression, Sample) %>%
group_by(Gene) %>%
arrange(Gene, desc(Expression))
**INPUT (dat)**
Gene Expression Sample
ENSG00000000027 2.79336700 HSB431
ENSG00000000938 0.83478860 HSB414
ENSG00000000003 2.40009100 HSB618
ENSG00000000938 1.75148448 HSB671
ENSG00000000938 1.52182467 HSB670
ENSG00000000938 0.62174432 HSB459
ENSG00000000003 2.81561500 HSB671
**EXPECTED OUTPUT**
Gene Expression Sample Rank
ENSG00000000003 2.81561500 HSB671 1
ENSG00000000003 2.79336700 HSB431 2
ENSG00000000027 2.79336700 HSB431 1
ENSG00000000938 1.75148448 HSB671 1
ENSG00000000938 1.52182467 HSB670 2
ENSG00000000938 0.83478860 HSB414 3
ENSG00000000938 0.62174432 HSB459 4
UPDATE
When trying:
dat %>%
group_by(Gene) %>%
mutate(Rank = dense_rank(Expression)) %>%
arrange(Gene, Expression, Rank)
I get:
Gene Sample Expression Rank
ENSG00000000003 HSB626 3.52200400 31107
ENSG00000000938 HSB152 -1.60663921 1585
ENSG00000000938 HSB425 -0.40209856 3536
ENSG00000000938 HSB627 -1.09598712 2244
ENSG00000000938 HSB645 -0.82846242 2666
ENSG00000000971 HSB154 4.61434903 53421
ENSG00000000971 HSB154 4.61434903 53421
ENSG00000000971 HSB154 4.61434903 53421
ENSG00000000971 HSB195 2.45561878 18041
ENSG00000000971 HSB222 5.54389646 79697
r dataframe ranking
asked Nov 28 '18 at 17:04
claudiadastclaudiadast
13711
I have the following input dataframe and would like to first group it by Gene and then arrange by descending Expression. Once I've done that, I'd like to add a Rank column that ranks each row per Gene according to the Expression value - so rows with higher Expression per gene get ranked higher.
I've already done the group by and arrange by part (below), but I'm struggling with how to do the ranking.
dat_sorted <- dat %>% select(Gene, Expression, Sample) %>%
group_by(Gene) %>%
arrange(Gene, desc(Expression))
**INPUT (dat)**
Gene Expression Sample
ENSG00000000027 2.79336700 HSB431
ENSG00000000938 0.83478860 HSB414
ENSG00000000003 2.40009100 HSB618
ENSG00000000938 1.75148448 HSB671
ENSG00000000938 1.52182467 HSB670
ENSG00000000938 0.62174432 HSB459
ENSG00000000003 2.81561500 HSB671
**EXPECTED OUTPUT**
Gene Expression Sample Rank
ENSG00000000003 2.81561500 HSB671 1
ENSG00000000003 2.79336700 HSB431 2
ENSG00000000027 2.79336700 HSB431 1
ENSG00000000938 1.75148448 HSB671 1
ENSG00000000938 1.52182467 HSB670 2
ENSG00000000938 0.83478860 HSB414 3
ENSG00000000938 0.62174432 HSB459 4
UPDATE
When trying:
dat %>%
group_by(Gene) %>%
mutate(Rank = dense_rank(Expression)) %>%
arrange(Gene, Expression, Rank)
I get:
Gene Sample Expression Rank
ENSG00000000003 HSB626 3.52200400 31107
ENSG00000000938 HSB152 -1.60663921 1585
ENSG00000000938 HSB425 -0.40209856 3536
ENSG00000000938 HSB627 -1.09598712 2244
ENSG00000000938 HSB645 -0.82846242 2666
ENSG00000000971 HSB154 4.61434903 53421
ENSG00000000971 HSB154 4.61434903 53421
ENSG00000000971 HSB154 4.61434903 53421
ENSG00000000971 HSB195 2.45561878 18041
ENSG00000000971 HSB222 5.54389646 79697
r dataframe ranking
r dataframe ranking
asked Nov 28 '18 at 17:04
claudiadastclaudiadast
13711
asked Nov 28 '18 at 17:04
claudiadastclaudiadast
13711
edited Nov 28 '18 at 17:20
claudiadast
asked Nov 28 '18 at 17:04
claudiadastclaudiadast
13711
asked Nov 28 '18 at 17:04
claudiadastclaudiadast
13711
asked Nov 28 '18 at 17:04
claudiadastclaudiadast
13711
13711
2
... %>% mutate(Rank = 1:n()), this relies on yourarrangeordering. Or using therankfunction (which ranks low to high, so we need a negative)... %>% mutate(Rank = rank(-Expression)), which just uses theExpressionvalues so it doesn't depend on the ordering. Alsorankhas several options for dealing with ties.
– Gregor
Nov 28 '18 at 17:07
@Gregor: Do you mind providing a complete example? I've tried variations of what you suggested but am still not having any luck.
– claudiadast
Nov 28 '18 at 17:32
2
From your edit it looks like you've loadedplyrafterdplyrand ignored the warnings. See this R-FAQ. Rundetach(package:plyr)or specifydplyr::mutateand it should work.
– Gregor
Nov 28 '18 at 17:34
add a comment |
2
... %>% mutate(Rank = 1:n()), this relies on yourarrangeordering. Or using therankfunction (which ranks low to high, so we need a negative)... %>% mutate(Rank = rank(-Expression)), which just uses theExpressionvalues so it doesn't depend on the ordering. Alsorankhas several options for dealing with ties.
– Gregor
Nov 28 '18 at 17:07
@Gregor: Do you mind providing a complete example? I've tried variations of what you suggested but am still not having any luck.
– claudiadast
Nov 28 '18 at 17:32
2
From your edit it looks like you've loadedplyrafterdplyrand ignored the warnings. See this R-FAQ. Rundetach(package:plyr)or specifydplyr::mutateand it should work.
– Gregor
Nov 28 '18 at 17:34
2
2
... %>% mutate(Rank = 1:n()), this relies on your arrange ordering. Or using the rank function (which ranks low to high, so we need a negative) ... %>% mutate(Rank = rank(-Expression)), which just uses the Expression values so it doesn't depend on the ordering. Also rank has several options for dealing with ties.– Gregor
Nov 28 '18 at 17:07
... %>% mutate(Rank = 1:n()), this relies on your arrange ordering. Or using the rank function (which ranks low to high, so we need a negative) ... %>% mutate(Rank = rank(-Expression)), which just uses the Expression values so it doesn't depend on the ordering. Also rank has several options for dealing with ties.– Gregor
Nov 28 '18 at 17:07
@Gregor: Do you mind providing a complete example? I've tried variations of what you suggested but am still not having any luck.
– claudiadast
Nov 28 '18 at 17:32
@Gregor: Do you mind providing a complete example? I've tried variations of what you suggested but am still not having any luck.
– claudiadast
Nov 28 '18 at 17:32
2
2
From your edit it looks like you've loaded
plyr after dplyr and ignored the warnings. See this R-FAQ. Run detach(package:plyr) or specify dplyr::mutate and it should work.– Gregor
Nov 28 '18 at 17:34
From your edit it looks like you've loaded
plyr after dplyr and ignored the warnings. See this R-FAQ. Run detach(package:plyr) or specify dplyr::mutate and it should work.– Gregor
Nov 28 '18 at 17:34
add a comment |
2 Answers
2
active
oldest
votes
0
We can use dense_rank
dat %>%
group_by(Gene) %>%
mutate(Rank = dense_rank(Expression)) %>%
arrange(Gene, Expression, Rank)
answered Nov 28 '18 at 17:07
akrunakrun
417k13205278
add a comment |
0
The following worked:
dplyr::mutate
dat_rank <- dat %>%
group_by(Gene) %>%
arrange(Gene, desc(Expression)) %>%
mutate(Rank = 1:n())
answered Nov 28 '18 at 17:42
claudiadastclaudiadast
13711
add a comment |
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0
We can use dense_rank
dat %>%
group_by(Gene) %>%
mutate(Rank = dense_rank(Expression)) %>%
arrange(Gene, Expression, Rank)
answered Nov 28 '18 at 17:07
akrunakrun
417k13205278
add a comment |
0
We can use dense_rank
dat %>%
group_by(Gene) %>%
mutate(Rank = dense_rank(Expression)) %>%
arrange(Gene, Expression, Rank)
answered Nov 28 '18 at 17:07
akrunakrun
417k13205278
add a comment |
0
0
0
We can use dense_rank
dat %>%
group_by(Gene) %>%
mutate(Rank = dense_rank(Expression)) %>%
arrange(Gene, Expression, Rank)
answered Nov 28 '18 at 17:07
akrunakrun
417k13205278
We can use dense_rank
dat %>%
group_by(Gene) %>%
mutate(Rank = dense_rank(Expression)) %>%
arrange(Gene, Expression, Rank)
answered Nov 28 '18 at 17:07
akrunakrun
417k13205278
answered Nov 28 '18 at 17:07
akrunakrun
417k13205278
answered Nov 28 '18 at 17:07
akrunakrun
417k13205278
answered Nov 28 '18 at 17:07
akrunakrun
417k13205278
417k13205278
add a comment |
add a comment |
0
The following worked:
dplyr::mutate
dat_rank <- dat %>%
group_by(Gene) %>%
arrange(Gene, desc(Expression)) %>%
mutate(Rank = 1:n())
answered Nov 28 '18 at 17:42
claudiadastclaudiadast
13711
add a comment |
0
The following worked:
dplyr::mutate
dat_rank <- dat %>%
group_by(Gene) %>%
arrange(Gene, desc(Expression)) %>%
mutate(Rank = 1:n())
answered Nov 28 '18 at 17:42
claudiadastclaudiadast
13711
add a comment |
0
0
0
The following worked:
dplyr::mutate
dat_rank <- dat %>%
group_by(Gene) %>%
arrange(Gene, desc(Expression)) %>%
mutate(Rank = 1:n())
answered Nov 28 '18 at 17:42
claudiadastclaudiadast
13711
The following worked:
dplyr::mutate
dat_rank <- dat %>%
group_by(Gene) %>%
arrange(Gene, desc(Expression)) %>%
mutate(Rank = 1:n())
answered Nov 28 '18 at 17:42
claudiadastclaudiadast
13711
answered Nov 28 '18 at 17:42
claudiadastclaudiadast
13711
answered Nov 28 '18 at 17:42
claudiadastclaudiadast
13711
answered Nov 28 '18 at 17:42
claudiadastclaudiadast
13711
13711
add a comment |
add a comment |
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2
... %>% mutate(Rank = 1:n()), this relies on yourarrangeordering. Or using therankfunction (which ranks low to high, so we need a negative)... %>% mutate(Rank = rank(-Expression)), which just uses theExpressionvalues so it doesn't depend on the ordering. Alsorankhas several options for dealing with ties.– Gregor
Nov 28 '18 at 17:07
@Gregor: Do you mind providing a complete example? I've tried variations of what you suggested but am still not having any luck.
– claudiadast
Nov 28 '18 at 17:32
2
From your edit it looks like you've loaded
plyrafterdplyrand ignored the warnings. See this R-FAQ. Rundetach(package:plyr)or specifydplyr::mutateand it should work.– Gregor
Nov 28 '18 at 17:34