I have a dataframe df
Reads Counts
aaaa 10
bbbb 20
cccc 25
and so on.
I want to calculate the number of reads which exceed a certain value of counts and plot that. Example I want a data frame that looks like
Counts>= #reads with Counts>=
1 3
2 3
3 3
11 2
20 2
21 1
and so on. Can you suggest how I can get such a dataframe and plot it.
Given the levels you want to plot at...
cutoffs <- 1:30
... you could do something like:
data.frame(cutoff=cutoffs, num.above=Reduce("+", lapply(dat$Counts, ">=", cutoffs)))
# cutoff num.above
# 1 1 3
# 2 2 3
# 3 3 3
# 4 4 3
# 5 5 3
# 6 6 3
# 7 7 3
# 8 8 3
# 9 9 3
# 10 10 3
# 11 11 2
# 12 12 2
# 13 13 2
# 14 14 2
# 15 15 2
# 16 16 2
# 17 17 2
# 18 18 2
# 19 19 2
# 20 20 2
# 21 21 1
# 22 22 1
# 23 23 1
# 24 24 1
# 25 25 1
# 26 26 0
# 27 27 0
# 28 28 0
# 29 29 0
# 30 30 0
Basically for each value in the original data frame you compute a vector of whether it's greater than or equal to each cutoff (using lapply with >=). Then you add them up (using Reduce with +), getting the total number greater than or equal to each cutoff.
Another option would be using outer/colSums
cutoff <- 1:30
data.frame(cutoff=cutoffs, num.above=colSums(outer(df$Counts, cutoffs, ">=")))
Related
I would like to create groups from a base by matching values.
I have the following data table:
now<-c(1,2,3,4,24,25,26,5,6,21,22,23)
before<-c(0,1,2,3,23,24,25,4,5,0,21,22)
after<-c(2,3,4,5,25,26,0,6,0,22,23,24)
df<-as.data.frame(cbind(now,before,after))
which reproduces the following data:
now before after
1 1 0 2
2 2 1 3
3 3 2 4
4 4 3 5
5 24 23 25
6 25 24 26
7 26 25 0
8 5 4 6
9 6 5 0
10 21 0 22
11 22 21 23
12 23 22 24
I would like to get:
now before after group
1 1 0 2 A
2 2 1 3 A
3 3 2 4 A
4 4 3 5 A
5 5 4 6 A
6 6 5 0 A
7 21 0 22 B
8 22 21 23 B
9 23 22 24 B
10 24 23 25 B
11 25 24 26 B
12 26 25 0 B
I would like to reach the answer to this without using a "for" loop becouse the real data is too large.
Any you could provide will be appreciated.
Here is one way. It is hard to avoid a for-loop as this is quite a tricky algorithm. The objection to them is often on the grounds of elegance rather than speed, but sometimes they are entirely appropriate.
df$group <- seq_len(nrow(df)) #assign each row to its own group
stop <- FALSE #indicates convergence
while(!stop){
pre <- df$group #group column at start of loop
for(i in seq_len(nrow(df))){
matched <- which(df$before==df$now[i] | df$after==df$now[i]) #check matches in before and after columns
group <- min(df$group[i], df$group[matched]) #identify smallest group no of matching rows
df$group[i] <- group #set to smallest group
df$group[matched] <- group #set to smallest group
}
if(identical(df$group, pre)) stop <- TRUE #stop if no change
}
df$group <- LETTERS[match(df$group, sort(unique(df$group)))] #convert groups to letters
#(just use match(...) to keep them as integers - e.g. if you have more than 26 groups)
df <- df[order(df$group, df$now),] #reorder as required
df
now before after group
1 1 0 2 A
2 2 1 3 A
3 3 2 4 A
4 4 3 5 A
8 5 4 6 A
9 6 5 0 A
10 21 0 22 B
11 22 21 23 B
12 23 22 24 B
5 24 23 25 B
6 25 24 26 B
7 26 25 0 B
My data looks like this:
x y
1 1
2 2
3 2
4 4
5 5
6 6
7 6
8 8
9 9
10 9
11 11
12 12
13 13
14 13
15 14
16 15
17 14
18 16
19 17
20 18
y is a grouping variable. I would like to see how well this grouping went.
Because of this I want to extract a sample of n pairs of cases that are grouped together by variable y
and n pairs of cases that are not grouped together by variable y. In order to calculate the number of
false positives and false negatives (either falsly grouped or not). How do I extract a sample of grouped pairs
and a sample of not-grouped pairs?
I would like the samples to look like this (for n=6) :
Grouped sample:
x y
2 2
3 2
9 9
10 9
15 14
17 14
Not-grouped sample:
x y
1 1
2 2
6 8
6 8
11 11
19 17
How would I go about this in R?
I'm not entirely clear on what you like to do, partly because I feel there is some context missing as to what you're trying to achieve. I also don't quite understand your expected output (for example, the not-grouped sample contains an entry 6 8 that does not exist in your original data...)
That aside, here is a possible approach.
# Maximum number of samples per group
n <- 3;
# Set fixed RNG seed for reproducibility
set.seed(2017);
# Grouped samples
df.grouped <- do.call(rbind.data.frame, lapply(split(df, df$y),
function(x) if (nrow(x) > 1) x[sample(min(n, nrow(x))), ]));
df.grouped;
# x y
#2.3 3 2
#2.2 2 2
#6.6 6 6
#6.7 7 6
#9.10 10 9
#9.9 9 9
#13.13 13 13
#13.14 14 13
#14.15 15 14
#14.17 17 14
# Ungrouped samples
df.ungrouped <- df[sample(nrow(df.grouped)), ];
df.ungrouped;
# x y
#7 7 6
#1 1 1
#9 9 9
#4 4 4
#3 3 2
#2 2 2
#5 5 5
#6 6 6
#10 10 9
#8 8 8
Explanation: Split df based on y, then draw min(n, nrow(x)) samples from subset x containing >1 rows; rbinding gives the grouped df.grouped. We then draw nrow(df.grouped) samples from df to produce the ungrouped df.ungrouped.
Sample data
df <- read.table(text =
"x y
1 1
2 2
3 2
4 4
5 5
6 6
7 6
8 8
9 9
10 9
11 11
12 12
13 13
14 13
15 14
16 15
17 14
18 16
19 17
20 18", header = T)
I have a data frame of GPS locations with a column of seconds. How can I split create a new column based on time-gaps? i.e. for this data.frame:
df <- data.frame(secs=c(1,2,3,4,5,6,7,10,11,12,13,14,20,21,22,23,24,28,29,31))
I would like to cut the data frame when there is a time gap between locations of 3 or more seconds seconds and create a new column entitled 'bouts' which gives a running tally of the number of sections to give a data frame looking like this:
id secs bouts
1 1 1
2 2 1
3 3 1
4 4 1
5 5 1
6 6 1
7 7 1
8 10 2
9 11 2
10 12 2
11 13 2
12 14 2
13 20 3
14 21 3
15 22 3
16 23 3
17 24 3
18 28 4
19 29 4
20 31 4
Use cumsum and diff:
df$bouts <- cumsum(c(1, diff(df$secs) >= 3))
Remember that logical values get coerced to numeric values 0/1 automatically and that diff output is always one element shorter than its input.
ID MON in out
2 1 23 12
3 1 23 12
7 1 33 22
1 2 22 11
2 2 111 100
1 3 21 10
2 3 22 11
2 4 111 100
7 4 21 10
2 5 31 20
7 2046 41 30
I have a large data set in this format. I want to extract column four for the value of column 1==2 and column 2 smaller then 5.
It's basic R.
df[,4][df[,1]==2 & df[,2]<5]
I have copied my code below. I start with a list of 50 small integers, representing the number of televisions owned by 50 families. My objective is shown in the object 'tv.final' below. My effort seems very wordy and inefficient.
Question: is there a better way to start with a list of 50 integers and end with a grouped data table with proportions? (Just taking my first baby steps with R, sorry for such a stupid question, but inquiring minds want to know.)
tv.data <- read.table("Tb02-08.txt",header=TRUE)
str(tv.data)
# 'data.frame': 50 obs. of 1 variable:
# $ TVs: int 1 1 1 2 6 3 3 4 2 4 ...
tv.table <- table(tv.data)
tv.table
# tv.data
# 0 1 2 3 4 5 6
# 1 16 14 12 3 2 2
tv.prop <- prop.table(tv.table)*100
tv.prop
# tv.data
# 0 1 2 3 4 5 6
# 2 32 28 24 6 4 4
tvs <- rbind(tv.table,tv.prop)
tvs
# 0 1 2 3 4 5 6
# tv.table 1 16 14 12 3 2 2
# tv.prop 2 32 28 24 6 4 4
tv.final <- t(tvs)
tv.final
# tv.table tv.prop
# 0 1 2
# 1 16 32
# 2 14 28
# 3 12 24
# 4 3 6
# 5 2 4
# 6 2 4
You can treat the object returned by table() as any other vector/matrix:
tv.table <- table(tv.data)
round(100 * tv.table/sum(tv.table))
That will give you the proportions in rounded percentage points.