I have a table were each sample has a unique identifier but also a section identifier. I want to extract all vs all distance comparisons for each section (this data comes from a second table)
eg table 1
Sample Section
1 1
2 1
3 1
4 2
5 2
6 3
table 2
sample sample distance
1 2 10
1 3 1
1 4 2
2 3 5
2 4 10
3 4 11
so my desired output is a list which has distance for: [1 vs 2], [1 vs 3], [2 vs 3], [4 vs 5] - ie all distance comparisons from table two for samples which share a section in table 1
I started trying to do this with nested for loops, but it quickly got messy.. Any ideas of a neat way to do this?
A solution using dplyr .
We can first create a data frame showing the combination of samples in each section.
library(dplyr)
table1_cross <- full_join(table1, table1, by = "Section") %>% # Full join by Section
filter(Sample.x != Sample.y) %>% # Remove records with same samples
rowwise() %>%
mutate(Sample.all = toString(sort(c(Sample.x, Sample.y)))) %>% # Create a column showing the combination between Sample.x and Sample.y
ungroup() %>%
distinct(Sample.all, .keep_all = TRUE) %>% # Remove duplicates in Sample.all
select(Sample1 = Sample.x, Sample2 = Sample.y, Section)
table1_cross
# # A tibble: 4 x 3
# Sample1 Sample2 Section
# <int> <int> <int>
# 1 1 2 1
# 2 1 3 1
# 3 2 3 1
# 4 4 5 2
We can then filter table2
by table1_cross
. table3
is the final output.
table3 <- table2 %>%
semi_join(table1_cross, by = c("Sample1", "Sample2")) # Filter table2 based on table1_corss
table3
# Sample1 Sample2 distance
# 1 1 2 10
# 2 1 3 1
# 3 2 3 5
DATA
table1 <- read.table(text = "Sample Section
1 1
2 1
3 1
4 2
5 2
6 3",
header = TRUE, stringsAsFactors = FALSE)
table2 <- read.table(text = "Sample1 Sample2 distance
1 2 10
1 3 1
1 4 2
2 3 5
2 4 10
3 4 11",
header = TRUE, stringsAsFactors = FALSE)
The OP has requested to find all distance comparisons from table2
for samples which share a section in table1
.
This can be achieved by two different approaches:
Sample1
and Sample2
each in table1
and keep only those rows of table2
where the section ids match. table1
and find the appropriate entries in table2
(if any). tmp <- merge(table2, table1, by.x = "Sample1", by.y = "Sample")
tmp <- merge(tmp, table1, by.x = "Sample2", by.y = "Sample")
tmp[tmp$Section.x == tmp$Section.y, c("Sample2", "Sample1", "distance")]
Sample2 Sample1 distance 1 2 1 10 2 3 1 1 3 3 2 5
dplyr
library(dplyr)
table2 %>%
inner_join(table1, by = c(Sample1 = "Sample")) %>%
inner_join(table1, by = c(Sample2 = "Sample")) %>%
filter(Section.x == Section.y) %>%
select(-Section.x, -Section.y)
Sample1 Sample2 distance 1 1 2 10 2 1 3 1 3 2 3 5
data.table
Using nested joins
library(data.table)
tmp <- setDT(table1)[setDT(table2), on = .(Sample == Sample1)]
table1[tmp, on = .(Sample == Sample2)][
Section == i.Section, .(Sample1 = i.Sample, Sample2 = Sample, distance)]
using merge() and chained data.table expressions
tmp <- merge(setDT(table2), setDT(table1), by.x = "Sample1", by.y = "Sample")
merge(tmp, table1, by.x = "Sample2", by.y = "Sample")[
Section.x == Section.y, -c("Section.x", "Section.y")]
Sample2 Sample1 distance 1: 2 1 10 2: 3 1 1 3: 3 2 5
table1_cross <- do.call(rbind, lst <- lapply(
split(table1, table1$Section),
function(x) as.data.frame(combinat::combn2(x$Sample))))
merge(table2, table1_cross, by.x = c("Sample1", "Sample2"), by.y = c("V1", "V2"))
Here, the handy combn2(x)
function is used which generates all combinations of the elements of x taken two at a time, eg,
combinat::combn2(1:3)
[,1] [,2] [1,] 1 2 [2,] 1 3 [3,] 2 3
The tedious part is to apply combn2()
to each group of Section
separately and to create a data.frame which can be merged, finally.
dplyr
This is a streamlined version of www's approach
full_join(table1, table1, by = "Section") %>%
filter(Sample.x < Sample.y) %>%
semi_join(x = table2, y = ., by = c(Sample1 = "Sample.x", Sample2 = "Sample.y"))
library(data.table)
setDT(table2)[setDT(table1)[table1, on = .(Section, Sample < Sample), allow = TRUE,
.(Section, Sample1 = x.Sample, Sample2 = i.Sample)],
on = .(Sample1, Sample2), nomatch = 0L]
Sample1 Sample2 distance Section 1: 1 2 10 1 2: 1 3 1 1 3: 2 3 5 1
Here, a non-equi join is used to create the unique combinations of Sample
for each Section
. This is equivalent to using combn2()
:
setDT(table1)[table1, on = .(Section, Sample < Sample), allow = TRUE,
.(Section, Sample1 = x.Sample, Sample2 = i.Sample)]
Section Sample1 Sample2 1: 1 NA 1 2: 1 1 2 3: 1 1 3 4: 1 2 3 5: 2 NA 4 6: 2 4 5 7: 3 NA 6
The NA
rows will be removed in the final join.
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