I have a data frame with a column that contains some elements that are lists. I would like to find out which rows of the data frame contain a keyword in that column.
The data frame, df, looks a bit like this
idstr tag
1 wl
2 other.to
3 other.from
4 c("wl","other.to")
5 wl
6 other.wl
7 c("ll","other.to")
The goal is to assign all of the rows with 'wl' in their tag to a new data frame. In this example, I would want a new data frame that looks like:
idstr tag
1 wl
4 c("wl","other.to")
5 wl
I tried something like this
df_wl <- df[which(is.element('wl',df$tag)),]
but this only returns the first element of the data frame (whether or not it contains 'wl'). I think the trouble lies in iterating through the rows and implementing the "is.element" function. Here are two implementations of the function and it's results:
is.element('wl',df$tag[[4]]) > TRUE
is.element('wl',df$tag[4]) > FALSE
How do you suggest I iterate through the dataframe to assign df_wl with it's proper values?
PS: Here's the dput:
structure(list(idstr = 1:7, tag = structure(c(6L, 5L, 4L, 2L, 6L, 3L, 1L), .Label = c("c(\"ll\",\"other.to\")", "c(\"wl\",\"other.to\")", "other.wl", "other.from", "other.to", "wl"), class = "factor")), .Names = c("idstr", "tag"), row.names = c(NA, -7L), class = "data.frame")
Based on your dput data. this may work. The regular expression (^wl$)|(\"wl\") matches wl from beginning to end, or any occurrence of "wl" (wrapped in double quotes)
df[grepl("(^wl$)|(\"wl\")", df$tag),]
# idstr tag
# 1 1 wl
# 4 4 c("wl","other.to")
# 5 5 wl
Related
I have a dataset with two columns containing the following: an indicator number and a hashcode
The only problem is that the columns have the same name, but the value can switch columns.
Now I want to merge the columns and keep the number (I don't care about the hashcode)
I saw this question: Merge two columns into one in r
and I tried the coalesce() function, but that is only for having NA values. Which I don't have. I looked at the unite function, but according to the cheat sheet documentation documentation here that doesn't what I'm looking for
My next try was the filter_at and other filter functions from the dplyr package Documentation here
But that only leaves 150 data points while at the start I have 61k data points.
Code of filter_at I tried:
data <- filter_at(data,vars("hk","hk_1"),all_vars(.>0))
I assumed that a #-string shall not be greater than 0, which seems to be true, but it removes more than intented.
I would like to keep hk or hk_1 value which is a number. The other one (the hash) can be removed. Then I want a new column which only contains those numbers.
Sample data
My data looks like this:
HK|HK1
190|#SP0839
190|#SP0340
178|#SP2949
#SP8390|177
#SP2240|212
What I would like to see:
HK
190
190
178
177
212
I hope this provides an insight into the data. There are more columns like description, etc which makes that 190 at the start are not doubles.
We can replace all the values that start with "#" to NA and then use coalesce to select non-NA value between HK and HK1.
library(dplyr)
df %>%
mutate_all(~as.character(replace(., grepl("^#", .), NA))) %>%
mutate(HK = coalesce(HK, HK1)) %>%
select(HK)
# HK
#1 190
#2 190
#3 178
#4 177
#5 212
data
df <- structure(list(HK = structure(c(4L, 4L, 3L, 2L, 1L), .Label = c("#SP2240",
"#SP8390", "178", "190"), class = "factor"), HK1 = structure(c(2L,
1L, 3L, 4L, 5L), .Label = c("#SP0340", "#SP0839", "#SP2949",
"177", "212"), class = "factor")), class = "data.frame", row.names = c(NA, -5L))
This question already has answers here:
Regular expressions (RegEx) and dplyr::filter()
(2 answers)
Closed 4 years ago.
I have a data.frame like this:
Client Product
1 VV_Brazil_Jul
2 VV_Brazil_Mar
5 VV_US_Jul
1 VV_JP_Apr
3 VV_CH_May
6 VV_Brazil_Aug
I would like to delete all rows with "Brazil".
You can do this using the grepl function and the ! to find the cases that are not matched:
# Create a dataframe where some cases have the product with Brazil as part of the value
df <- structure(list(Client = c(1L, 2L, 5L, 1L, 3L, 6L),
Product = c("VV_Brazil_Jul", "VV_Brazil_Mar", "VV_US_Jul", "VV_JP_Apr", "VV_CH_May", "VV_Brazil_Aug")),
row.names = c(NA, -6L), class = c("data.table", "data.frame"))
# Display the original dataframe in the Console
df
# Limit the dataframe to cases which do not have Brazil as part of the product
df <- df[!grepl("Brazil", df$Product, ignore.case = TRUE),]
# Display the revised dataframe in the Console
df
You can do the same thing with the tidyverse collection
dplyr::slice(df, -stringr::str_which(df$Product, "Brazil"))
I'm trying to subset data in R by certain characters in a field and cannot find the correct regex logic to get what I need. I need to subset records for which the ID contains either:
Just "AB"
"AB" and "ABC"
But NOT fields with ONLY "ABC"
These patterns fall within any part of the field (beginning, middle, end) in this data set and have no certain separators.
Example dataset TEST:
Record ID value
1 blueAB_ABC 7
2 green_ABCblue 9
3 ABC_green 45
4 green_AB 23
5 CD_red 45
So for this example I would want to subset records 1 and 4.
I've gotten as far as returning those with just AB and excluding ABC, but cannot seem to find the proper regex to get all with "AB" and potentially "ABC".
AB_set <- subset(TEST, grepl("*AB", ID) & !grepl("*ABC", ID) )
Record ID value
4 green_AB 23
What I'm hoping to get:
Record ID value
1 blueAB_ABC 7
4 green_AB 23
EDIT: Just to clarify, I updated the dataset to show that the pattern in question may fall next to other characters than an underscore, or may not necessarily occur at the beginning/end (as previously noted, "no certain separators").
You can get this by specifying that "AB" should be surrounded by either underscore or a word boundary.
df[grepl("(\\b|_)AB(\\b|_)", df$ID),]
Record ID value
1 1 blue_AB_ABC 7
4 4 green_AB 23
"ABC" is not needed because "AB" is always required to be matched. The following matches AB only if it is surrounded by underscore or it starts or ends an ID:
AB_set <- subset(TEST, grepl("(^|_)AB(_|$)", TEST$ID))
Result:
Record ID value
1 1 blue_AB_ABC 7
4 4 green_AB 23
Data:
TEST = structure(list(Record = 1:5, ID = structure(c(2L, 5L, 1L, 4L,
3L), .Label = c("ABC_green", "blue_AB_ABC", "CD_red", "green_AB",
"green_ABC_blue"), class = "factor"), value = c(7L, 9L, 45L,
23L, 45L)), .Names = c("Record", "ID", "value"), class = "data.frame", row.names = c(NA,
-5L))
I have 2 dataframe sharing the same rows IDs but with different columns
Here is an example
chrom coord sID CM0016 CM0017 CM0018
7 10 3178881 SP_SA036,SP_SA040 0.000000000 0.000000000 0.0009923
8 10 38894616 SP_SA036,SP_SA040 0.000434783 0.000467464 0.0000970
9 11 104972190 SP_SA036,SP_SA040 0.497802888 0.529319536 0.5479003
and
chrom coord sID CM0001 CM0002 CM0003
4 10 3178881 SP_SA036,SA040 0.526806527 0.544927536 0.565610860
5 10 38894616 SP_SA036,SA040 0.009049774 0.002849003 0.002857143
6 11 104972190 SP_SA036,SA040 0.451612903 0.401617251 0.435318275
I am trying to create a composite boxplot figure where I have in x axis the chrom and coord combined (so 3 points) and for each x value 2 boxplots side by side corresponding to the two dataframes ?
What is the best way of doing this ? Should I merge the two dataframes together somehow in order to get only one and loop over the boxplots rendering by 3 columns ?
Any idea on how this can be done ?
The problem is that the two dataframes have the same number of rows but can differ in number of columns
> dim(A)
[1] 99 20
> dim(B)
[1] 99 28
I was thinking about transposing the dataframe in order to get the same number of column but got lost on how to this properly
Thanks in advance
UPDATE
This is what I tried to do
I merged chrom and coord columns together to create a single ID
I used reshape t melt the dataframes
I merged the 2 melted dataframe into a single one
the head looks like this
I have two variable A2 and A4 corresponding to the 2 dataframes
then I created a boxplot such using this
ggplot(A2A4, aes(factor(combine), value)) +geom_boxplot(aes(fill = factor(variable)))
I think it solved my problem but the boxplot looks very busy with 99 x values with 2 boxplots each
So if these are your input tables
d1<-structure(list(chrom = c(10L, 10L, 11L),
coord = c(3178881L, 38894616L, 104972190L),
sID = structure(c(1L, 1L, 1L), .Label = "SP_SA036,SP_SA040", class = "factor"),
CM0016 = c(0, 0.000434783, 0.497802888), CM0017 = c(0, 0.000467464,
0.529319536), CM0018 = c(0.0009923, 9.7e-05, 0.5479003)), .Names = c("chrom",
"coord", "sID", "CM0016", "CM0017", "CM0018"), class = "data.frame", row.names = c("7",
"8", "9"))
d2<-structure(list(chrom = c(10L, 10L, 11L), coord = c(3178881L,
38894616L, 104972190L), sID = structure(c(1L, 1L, 1L), .Label = "SP_SA036,SA040", class = "factor"),
CM0001 = c(0.526806527, 0.009049774, 0.451612903), CM0002 = c(0.544927536,
0.002849003, 0.401617251), CM0003 = c(0.56561086, 0.002857143,
0.435318275)), .Names = c("chrom", "coord", "sID", "CM0001",
"CM0002", "CM0003"), class = "data.frame", row.names = c("4",
"5", "6"))
Then I would combine and reshape the data to make it easier to plot. Here's what i'd do
m1<-melt(d1, id.vars=c("chrom", "coord", "sID"))
m2<-melt(d2, id.vars=c("chrom", "coord", "sID"))
dd<-rbind(cbind(m1, s="T1"), cbind(m2, s="T2"))
mm$pos<-factor(paste(mm$chrom,mm$coord,sep=":"),
levels=do.call(paste, c(unique(dd[order(dd[[1]],dd[[2]]),1:2]), sep=":")))
I first melt the two input tables to turn columns into rows. Then I add a column to each table so I know where the data came from and rbind them together. And finally I do a bit of messy work to make a factor out of the chr/coord pairs sorted in the correct order.
With all that done, I'll make the plot like
ggplot(mm, aes(x=pos, y=value, color=s)) +
geom_boxplot(position="dodge")
and it looks like
I imagine that there's some way to do this with sqldf, though I'm not familiar with the syntax of that package enough to get this to work. Here's the issue:
I have two data frames, each of which describe genomic regions and contain some other data. I have to combine the two if the region described in the one df falls within the region of the other df.
One df, g, looks like this (though my real data has other columns)
start_position end_position
1 22926178 22928035
2 22887317 22889471
3 22876403 22884442
4 22862447 22866319
5 22822490 22827551
And another, l, looks like this (this sample has a named column)
name start end
101 GRMZM2G001024 11149187 11511198
589 GRMZM2G575546 24382534 24860958
7859 GRMZM2G441511 22762447 23762447
658 AC184765.4_FG005 26282236 26682919
14 GRMZM2G396835 10009264 10402790
I need to merge the two dataframes if the values from the start_position OR end_position columns in g fall within the start-end range in l, returning only the columns in l that have a match. I've been trying to get findInterval() to do the job, but haven't been able to return a merged DF. Any ideas?
My data:
g <- structure(list(start_position = c(22926178L, 22887317L, 22876403L,
22862447L, 22822490L), end_position = c(22928035L, 22889471L,
22884442L, 22866319L, 22827551L)), .Names = c("start_position",
"end_position"), row.names = c(NA, 5L), class = "data.frame")
l <- structure(list(name = structure(c(2L, 12L, 9L, 1L, 8L), .Label = c("AC184765.4_FG005",
"GRMZM2G001024", "GRMZM2G058655", "GRMZM2G072028", "GRMZM2G157132",
"GRMZM2G160834", "GRMZM2G166507", "GRMZM2G396835", "GRMZM2G441511",
"GRMZM2G442645", "GRMZM2G572807", "GRMZM2G575546", "GRMZM2G702094"
), class = "factor"), start = c(11149187L, 24382534L, 22762447L,
26282236L, 10009264L), end = c(11511198L, 24860958L, 23762447L,
26682919L, 10402790L)), .Names = c("name", "start", "end"), row.names = c(101L,
589L, 7859L, 658L, 14L), class = "data.frame")