[R] Correlation between matrices

[Dennis Murphy]

Hi:

I don't think you want to keep these objects separate; it's better to
combine everything into a data frame. Here's a variation of your
example - the x variable ends up being a mouse, but you may have
another variable that's more appropriate to plot so take this as a
starting point. One plot uses the ggplot2 package, the other uses the
lattice and latticeExtra packages.

library('ggplot2')
regions = c('cortex', 'hippocampus', 'brain_stem', 'mid_brain',
            'cerebellum')
mice = paste('mouse', 1:5, sep='')
elem <- c('Cu', 'Fe', 'Zn', 'Ca', 'Enzyme')

# Generate a data frame from the combinations of
# mice, regions and elem:
d <- data.frame(expand.grid(mice = mice, regions = regions,
                            elem = elem), y = rnorm(125))
# Create a numeric version of mice
d$mouse <- as.numeric(d$mice)

# A function to return regression coefficients
coefun <- function(df) coef(lm(y ~ mouse), data = df)
# Apply to all regions * elem combinations
coefs <- ddply(d, .(regions, elem), coefun)
names(coefs) <- c('regions', 'elem', 'b0', 'b1')

# Generate the plot using package ggplot2:
ggplot(d, aes(x = mouse, y = y)) +
   geom_point(size = 2.5) +
   geom_abline(data = coefs, aes(intercept = b0, slope = b1),
                             size = 1) +
   facet_grid(elem ~ regions)

# Same plot in lattice:
library('lattice')
library('latticeExtra')
p <- xyplot(y ~ mouse | elem + regions, data = d, type = c('p', 'r'),
         layout = c(5, 5))


HTH,
Dennis

On Sat, Nov 5, 2011 at 10:49 AM, Kaiyin Zhong <kindlychung at gmail.com> wrote:
>> regions = c('cortex', 'hippocampus', 'brain_stem', 'mid_brain',
> 'cerebellum')
>> mice = paste('mouse', 1:5, sep='')
>> for (n in c('Cu', 'Fe', 'Zn', 'Ca', 'Enzyme')) {
> +   assign(n, as.data.frame(replicate(5, rnorm(5))))
> + }
>> names(Cu) = names(Zn) = names(Fe) = names(Ca) = names(Enzyme) = regions
>> row.names(Cu) = row.names(Zn) = row.names(Fe) = row.names(Ca) =
> row.names(Enzyme) = mice
>> Cu
>           cortex hippocampus brain_stem  mid_brain cerebellum
> mouse1 -0.5436573 -0.31486713  0.1039148 -0.3908665 -1.0849112
> mouse2  1.4559136  1.75731752 -2.1195118 -0.9894767  0.3609033
> mouse3 -0.6735427 -0.04666507  0.9641000  0.4683339  0.7419944
> mouse4  0.6926557 -0.47820023  1.3560802  0.9967562 -1.3727874
> mouse5  0.2371585  0.20031393 -1.4978517  0.7535148  0.5632443
>> Zn
>            cortex hippocampus brain_stem  mid_brain  cerebellum
> mouse1 -0.66424043   0.6664478  1.1983546  0.0319403  0.41955740
> mouse2 -1.14510448   1.5612235  0.3210821  0.4094753  1.01637466
> mouse3 -0.85954416   2.8275458 -0.6922565 -0.8182307 -0.06961242
> mouse4  0.03606034  -0.7177256  0.7067217  0.2036655 -0.25542524
> mouse5  0.67427572   0.6171704  0.1044267 -1.8636174 -0.07654666
>> Fe
>           cortex hippocampus  brain_stem  mid_brain cerebellum
> mouse1  1.8337008   2.0884261  0.29730413 -1.6884804  0.8336137
> mouse2 -0.2734139  -0.5728439  0.63791556 -0.6232828 -1.1352224
> mouse3 -0.4795082   0.1627235  0.21775206  1.0751584 -0.5581422
> mouse4  1.7125147  -0.5830600  1.40597896 -0.2815305  0.3776360
> mouse5 -0.3469067  -0.4813120 -0.09606797  1.0970077 -1.1234038
>> Ca
>           cortex hippocampus  brain_stem   mid_brain cerebellum
> mouse1 -0.7663354   0.8595091  1.33803798 -1.17651576  0.8299963
> mouse2 -0.7132260  -0.2626811  0.08025079 -2.40924271  0.7883005
> mouse3 -0.7988904  -0.1144639 -0.65901136  0.42462227  0.7068755
> mouse4  0.3880393   0.5570068 -0.49969135  0.06633009 -1.3497228
> mouse5  1.0077684   0.6023264 -0.57387762  0.25919461 -0.9337281
>> Enzyme
>           cortex hippocampus  brain_stem  mid_brain cerebellum
> mouse1  1.3430936   0.5335819 -0.56992947  1.3565803 -0.8323391
> mouse2  1.0520850  -1.0201124  0.89600005  1.4719880  1.0854768
> mouse3 -0.2802482   0.6863323 -1.37483570 -0.7790174  0.2446761
> mouse4 -0.1916415  -0.4566571  1.93365932  1.3493848  0.2130424
> mouse5 -1.0349593  -0.1940268 -0.07216321 -0.2968288  1.7406905
>
> In each anatomic region, I would like to calculate the correlation between
> Enzyme activity and each of the concentrations of Cu, Zn, Fe, and Ca, and
> do a scatter plot with a tendency line, organizing those plots into a grid.
> See the image below for the desired effect:
> http://postimage.org/image/62brra6jn/
> How can I achieve this?
>
> Thank you in advance.
>
>        [[alternative HTML version deleted]]
>
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