I have a data frame like below.
dat <- data.frame(v1=c("a","b","c","c","a","w","f"),
v2=c("z","a","a","w","p","e","h"))
v1 v2
1 a z
2 b a
3 c a
4 c w
5 a p
6 w e
7 f h
I want to add a group column based on whether these letters appear in the same row.
v1 v2 gp
1 a z 1
2 b a 1
3 c a 1
4 c w 1
5 a p 1
6 w e 1
7 f h 2
My idea is to first assign the first row to group 1, and then any row that v1 or v2 is "a" or "z" will also be assigned to group 1.
There are scenarios like row 3 and 4, where c is assigned to group 1, because, in row 3, v2 is "a". And "w" is assigned to group 1 because in row 4 v1 is "c", which is assigned to group 1 previously. But my list is very long, so I cannot keep checking all the "descendants".
I wonder if there is a way to group these letters, and return a list with group number. Something like the below table will do.
letter gp
a 1
b 1
c 1
e 1
f 2
h 2
w 1
z 1
One way to solve this is to consider the letters as vertices of a graph and being in the same row as a link between the vertices. Then what you are asking for is the connected components of the graph. All of that is easy using the igraph package in R.
library(igraph)
G = graph_from_edgelist(as.matrix(dat), directed=FALSE)
letters = sort(unique(c(as.character(dat$v1), as.character(dat$v2))))
(gp = components(G)$membership[letters])
a b c e f h p w z
1 1 1 1 2 2 1 1 1
If you want a data.frame containing this information
(Groups = data.frame(letters, gp, row.names=NULL))
letters gp
1 a 1
2 b 1
3 c 1
4 e 1
5 f 2
6 h 2
7 p 1
8 w 1
9 z 1
In order to think through why this works, it may help you to look at the graph that was created and think how that represents your problem.
Related
I would like to generate indices to group observations based on two columns. But I want groups to be made of observation that share, at least one observation in commons.
In the data below, I want to check if values in 'G1' and 'G2' are connected directly (appear on the same row), or indirectly via other intermediate values. The desired grouping variable is shown in 'g'.
For example, A is directly linked to Z (row 1) and X (row 2). A is indirectly linked to 'B' via X (A -> X -> B), and further linked to Y via X and B (A -> X -> B -> Y).
dt <- data.frame(id = 1:10,
G1 = c("A","A","B","B","C","C","C","D","E","F"),
G2 = c("Z","X","X","Y","W","V","U","s","T","T"),
g = c(1,1,1,1,2,2,2,3,4,4))
dt
# id G1 G2 g
# 1 1 A Z 1
# 2 2 A X 1
# 3 3 B X 1
# 4 4 B Y 1
# 5 5 C W 2
# 6 6 C V 2
# 7 7 C U 2
# 8 8 D s 3
# 9 9 E T 4
# 10 10 F T 4
I tried with group_indices from dplyr, but haven't managed it.
Using igraph get membership, then map on names:
library(igraph)
# convert to graph, and get clusters membership ids
g <- graph_from_data_frame(df1[, c(2, 3, 1)])
myGroups <- components(g)$membership
myGroups
# A B C D E F Z X Y W V U s T
# 1 1 2 3 4 4 1 1 1 2 2 2 3 4
# then map on names
df1$group <- myGroups[df1$G1]
df1
# id G1 G2 group
# 1 1 A Z 1
# 2 2 A X 1
# 3 3 B X 1
# 4 4 B Y 1
# 5 5 C W 2
# 6 6 C V 2
# 7 7 C U 2
# 8 8 D s 3
# 9 9 E T 4
# 10 10 F T 4
Say we have a data frame with a factor (Group) that is a grouping variable for a list of IDs:
set.seed(123)
data <- data.frame(Group = factor(sample(5,10, replace = T)),
ID = c(1:10))
In this example, the ID's belong to one of 5 Groups, labeled 1:5. We simply want to replace 1:5 with A:E. In other words, if Group == 1, we want to change it to A, if Group == 2, we want to change it to B, and so on. What is the simplest way to achieve this?
You may assign new labels= in a names list using factor once again.
data$Group1 <- factor(data$Group, labels=list("1"="A", "2"="B", "3"="C", "4"="D", "5"="E"))
## more succinct:
data$Group2 <- factor(data$Group, labels=setNames(list("A", "B", "C", "D", "E"), 1:5))
data
# Group ID Group1 Group2 Group3
# 1 3 1 C C C
# 2 3 2 C C C
# 3 2 3 B B B
# 4 2 4 B B B
# 5 3 5 C C C
# 6 5 6 E E E
# 7 4 7 D D D
# 8 1 8 A A A
# 9 2 9 B B B
# 10 3 10 C C C
This for general, if indeed capital letters are wanted see #RonakShah's solution.
You can use the built-in constant in R LETTERS :
data$new_group <- LETTERS[data$Group]
data
# Group ID new_group
#1 3 1 C
#2 3 2 C
#3 2 3 B
#4 2 4 B
#5 3 5 C
#6 5 6 E
#7 4 7 D
#8 1 8 A
#9 2 9 B
#10 3 10 C
Created a new column (new_group) here for comparison purposes. You can overwrite the same column if you wish to.
I have a dataframe that looks something like this, where each row represents a samples, and has repeats of the the same strings
> df
V1 V2 V3 V4 V5
1 a a d d b
2 c a b d a
3 d b a a b
4 d d a b c
5 c a d c c
I want to be able to create a new dataframe, where ideally the headers would be the string variables in the previous dataframe (a, b, c, d) and the contents of each row would be the number of occurrences of each the respective variable from
the original dataframe. Using the example from above, this would look like
> df2
a b c d
1 2 1 0 2
2 2 1 1 1
3 2 1 0 1
4 1 1 1 2
5 1 0 3 1
In my actual dataset, there are hundreds of variables, and thousands of samples, so it'd be ideal if I could automatically pull out the names from the original dataframe, and alphabetize them into the headers for the new dataframe.
You may try
library(qdapTools)
mtabulate(as.data.frame(t(df)))
Or
mtabulate(split(as.matrix(df), row(df)))
Or using base R
Un1 <- sort(unique(unlist(df)))
t(apply(df ,1, function(x) table(factor(x, levels=Un1))))
You can stack the columns and then use table:
table(cbind(id = 1:nrow(mydf),
stack(lapply(mydf, as.character)))[c("id", "values")])
# values
# id a b c d
# 1 2 1 0 2
# 2 2 1 1 1
# 3 2 2 0 1
# 4 1 1 1 2
# 5 1 0 3 1
I have a data.frame df
> df
V1 V2
1 a b
2 a e
3 a f
4 b c
5 b e
6 b f
7 c d
8 c g
9 c h
10 d g
11 d h
12 e f
13 f g
14 g h
I found the frequency of each element's occurrence considering column V1 and sorted the Freq column in ascending order
>dfFreq <- as.data.frame(table(df$V1))
Var1 Freq
1 a 3
2 b 3
3 c 3
4 d 2
5 e 1
6 f 1
7 g 1
>dfFreqSorted <- dfFreq[order(dfFreq$Freq),]
Var1 Freq
5 e 1
6 f 1
7 g 1
4 d 2
1 a 3
2 b 3
3 c 3
Now what i want to do is to create a new data.frame based on original data.frame such that each "Var1" item in "dfFreqSorted" is used according to it's Freq but once every time going from the top of "dfFreqSorted" to the bottom which would give the result below:
So consider the first Var1 item which is "e" so the first matching row of "e" in V1 column of df is (e,f) which would be the first item in the new data.frame.
I figured that this can be done using:
>subset(df, V1==dfFreqSorted$Var[1])[1,]
V1 V2
12 e f
So if i used a for loop and looped through all the elements in the Var1 column of dfFreqSorted and used the subset command above and rbind the returned result into another data.frame I would have something like below
V1 V2
12 e f
13 f g
14 g h
10 d g
1 a b
4 b c
7 c d
Now this result shows each Var1 item once. I need the remaining rows as shown below such that after finishing first iteration of all the rows of Var1 once, the loop should go again to the beginning and check the frequency of all Var1 whose frequency is more than 1 now and find the next row from df for that element so the remaining rows that should be produced in the same data.frame as shown below:
11 d h
2 a e
5 b e
8 c g
3 a f
6 b f
9 c h
As you can see above that all elements are considered in Var1 whose frequency is 1 are used first then those whose frequency is greater than 1 (i.e 2) and are used once then in the next iteration those are used whose freq is greater than 2 (i.e 3) are used. Used such that corresponding unused row of that element is fetched from df.
So in short all the elements of df are arranged in anew data.frame such that elements are used in ascending order of their frequencies but used once first and then twice or thrice in every iteration based on what their frequency is.
I am not asking for the whole code just few guidelines of how i can achieve the objective. Thanks in advance.
Hello #akrun i am a beginner so the solution might be really a beginner level approach but it solved my problem perfectly fine.
> a<-read.table("isnodes.txt")
> a
V1 V2
1 a b
2 a e
3 a f
4 b c
5 b e
6 b f
7 c d
8 c g
9 c h
10 d g
11 d h
12 e f
13 f g
14 g h
> aF<-as.data.frame(table(a$V1))
> aF
Var1 Freq
1 a 3
2 b 3
3 c 3
4 d 2
5 e 1
6 f 1
7 g 1
> aFsorted <- aF[order(aF$Freq),]
> aFsorted
Var1 Freq
5 e 1
6 f 1
7 g 1
4 d 2
1 a 3
2 b 3
3 c 3
> sortedEdgeList <- a[-c(1:nrow(a)),]
> sortedEdgeList
[1] V1 V2
<0 rows> (or 0-length row.names)
> aFsorted <- cbind(aFsorted, Used=0)
> aFsorted
Var1 Freq Used
5 e 1 0
6 f 1 0
7 g 1 0
4 d 2 0
1 a 3 0
2 b 3 0
3 c 3 0
> maxFreq <- max(aFsorted$Freq)
> maxFreq
[1] 3
> for(i in 1:maxFreq){
+ rows<-nrow(aFsorted)
+ for(j in 1:rows){
+ Var1Value<-aFsorted$Var[j]
+ Var1Edge<-a[match(aFsorted$Var1[j],a$V1),]
+ sortedEdgeList<-rbind(sortedEdgeList,Var1Edge)
+ a<-a[!(a$V1==Var1Edge$V1 & a$V2==Var1Edge$V2),]
+ aFsorted$Used[j]=aFsorted$Used[j]+1
+ }
+ if(aFsorted$Used==aFsorted$Freq){
+ aFsorted<-aFsorted[!(aFsorted$Used==aFsorted$Freq),]
+ }
+ }
Warning messages:
1: In if (aFsorted$Used == aFsorted$Freq) { :
the condition has length > 1 and only the first element will be used
2: In if (aFsorted$Used == aFsorted$Freq) { :
the condition has length > 1 and only the first element will be used
3: In if (aFsorted$Used == aFsorted$Freq) { :
the condition has length > 1 and only the first element will be used
> sortedEdgeList
V1 V2
12 e f
13 f g
14 g h
10 d g
5 a b
4 b c
7 c d
11 d h
2 a e
51 b e
8 c g
3 a f
6 b f
9 c h
I'm not sure this is what you want, but it might be close. It helps conceptually to keep the frequencies in the original data frame.
library("plyr")
set.seed(3)
df <- data.frame(V1 = sample(letters[1:10], 20, replace = TRUE),
V2 = sample(letters[1:10], 20, replace = TRUE),
stringsAsFactors = FALSE)
df$freqV1 <- NA_integer_
for (i in 1:nrow(df)) {
df$freqV1[i] <- length(grep(pattern = df$V1[i], x = df$V1))
}
df2 <- arrange(df, freqV1, V2) # you may want just arrange(df, freqV1)
which gives:
V1 V2 freqV1
1 h c 1
2 d a 2
3 d b 2
4 c c 2
5 c j 2
6 b c 3
7 g c 3
8 b f 3
9 g h 3
10 g h 3
11 b i 3
12 i a 4
13 i c 4
14 i d 4
15 i f 4
16 f b 5
17 f d 5
18 f d 5
19 f e 5
20 f f 5
Suppose I have a dataframe 'H', like so
C1 C2
a 1
b 1
c 2
d 3
e 4
f 4
g 5
and a list X (as.factor) that goes
"1" "2" "4"
Using the match command,
X2=H[match(X,H$C2),]
only reduces H to three rows and only one instance of each element of X is present (a,c,e). What command should I employ to reduce H to X such that all instances of elements found in X are present (i.e, the reduced table should contain a,b,c,e,f)?
Cheers.
> H[H$C2 %in% X,]
C1 C2
1 a 1
2 b 1
3 c 2
5 e 4
6 f 4