Masi - 1 year ago 117
R Question

# How to create NxM Corr matrix from Column 2 of 2xN signals in R?

I have 2x N amount of 1D Signals in

`files`
where Column 1 is Signal 1 and Column 2 Signal 2.
Code 1 is simplified example about 1x N amount of 1D signals, while Code 2 is the actual target with two pieces of pseudocode about:

1. to create two dimensional vector (
`files[[i]] = i,i+1`
) - just two integer data units in each row separated by comma, and

2. and then accessing the data there later (
`tcrossprod( files[[]][, 2], files[[]][, 2] )`
) where I cannot refer to all columns 2 of all signals

Simplified Code 1 works as expected

``````## Example with 1D vector in Single column
N <- 7
files <- vector("list", N)
# Make a list of two column data
for (i in 1:N) {
files[[i]] = i
}

str(files)

# http://stackoverflow.com/a/40323768/54964
tcrossprod( files, files )
``````

Code 2 is pseudocode but target

``````## Example with 2x1D vectors in two columns
N <- 7
files <- vector("list", N)
# Make a list of two column data
for (i in 1:N) {
files[[i]] = i,i+1 # PSEUDOCODE
}

str(files)

# access one signal single columns by files[[1]][,1] and files[[1]][,2]
tcrossprod( files[[]][, 2], files[[]][, 2] ) # PSEUDOCODE
``````

Assume Vector 1 dimensions are Nx1 and Vector 1 1xM.
Each cell, accessed for instance for Signal 2 Column 2 by
`files[[1]][,2]`
contains 1D signal.
Mutiply all such signals of Column 2 by
`trossprod`
, you should get the expected result:
`NxM`
matrix.

## Mathematical description

Data: a list of two columns, where first column is 1D signal; 2nd column is improved 1D signal. I want to compare those improved 1D signals all together in the matrix.
Expected output

``````   cor      Improved 1 Improved 2 ...
Improved 1  1          0.55
Improved 2  0.111      1
...
``````

I am not tied to any particular R data structures .

Column and cell are just my descriptions of the items in the data units. So not precise because I am newbie in R.

Output of tchakravarty's graphic code in my system where you see x-axis is correct but not y-axis

OS: Debian 8.5

R: 3.1.1

I am still not sure of your question, so I will first try to make sure of the data structure that you have in mind.

I have created a list of length M (= 100) each element of which with an N x 2 matrix (where N = 1000) which represents the 2D signals.

``````N = 1000
li_matrices = setNames(
lapply(paste("Improved", 1:100), function(x) matrix(rnorm(N*2), nrow = N, ncol = 2, byrow = TRUE)),
paste("Improved", 1:100))

> str(li_matrices, list.len = 5, max.level = 1)
List of 100
\$ Improved 1  : num [1:1000, 1:2] 0.228 -0.44 0.713 -0.118 -0.918 ...
\$ Improved 2  : num [1:1000, 1:2] 0.928 0.362 -0.105 -0.1 0.165 ...
\$ Improved 3  : num [1:1000, 1:2] 0.0881 -0.1466 1.8549 -0.3376 -1.1626 ...
\$ Improved 4  : num [1:1000, 1:2] 0.0575 -0.7809 0.4221 0.5378 -0.7882 ...
\$ Improved 5  : num [1:1000, 1:2] 0.6739 1.4515 -0.0704 -0.1596 0.2157 ...
[list output truncated]
``````

Then, I have extracted the second dimension of the signals from each of the M list elements, and computed their correlations across the M replicates.

``````> cor(sapply(li_matrices, function(x) x[, 2]))
Improved 1    Improved 2    Improved 3    Improved 4    Improved 5    Improved 6    Improved 7
Improved 1    1.0000000000 -0.0181724914  0.0307864778 -0.0235266506  0.0681155904 -0.0654758679 -0.0416660418
Improved 2   -0.0181724914  1.0000000000  0.0837086793 -0.0310760562  0.0035757641 -0.0303866471 -0.0345608009
Improved 3    0.0307864778  0.0837086793  1.0000000000 -0.0093528744  0.0282039040 -0.0525328267  0.0410787784
Improved 4   -0.0235266506 -0.0310760562 -0.0093528744  1.0000000000 -0.0139707732 -0.0145970712 -0.0022037703
Improved 5    0.0681155904  0.0035757641  0.0282039040 -0.0139707732  1.0000000000 -0.0406468255  0.0381800143
Improved 6   -0.0654758679 -0.0303866471 -0.0525328267 -0.0145970712 -0.0406468255  1.0000000000 -0.0534592829
Improved 7   -0.0416660418 -0.0345608009  0.0410787784 -0.0022037703  0.0381800143 -0.0534592829  1.0000000000
Improved 8   -0.0320972342 -0.0344929079 -0.0204718584 -0.0007383034  0.0223386392 -0.0361548831  0.0090484961
Improved 9    0.0068743021 -0.0109232340  0.0071627901  0.0102613137  0.0265829001 -0.0443782611  0.0266421500
Improved 10  -0.0228804070 -0.0163596866  0.0066448268  0.0137962914  0.0357421845  0.0403325013 -0.0391002841
``````

# Edit:

Here is the plotting code requested by OP:

``````m_corr = cor(sapply(li_matrices, function(x) x[, 2]))

m_corr %>%
as.data.frame() %>%
rownames_to_column(var = "Var1") %>%
as_data_frame() %>%
gather(key = Var2, value = Value, -Var1) %>%
ggplot(
aes(
x = reorder(Var1, as.numeric(gsub("Improved ", "", Var1))),
y = reorder(Var2, as.numeric(gsub("Improved ", "", Var2))),
fill = Value
)
) +
geom_tile() +
theme_bw() +
theme(
axis.text.x = element_text(angle = 90, size = 5, hjust = 1),
axis.text.y = element_text(size = 5)
) +
xlab("Variable 1") +
ylab("Variable 2")
``````

This gives:

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