Created
May 21, 2013 17:51
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originally from: http://groups.google.com/group/ggplot2/attach/6bf632a9718dddd6/ggcorplot.R?part=2 linked to from here: http://www.r-bloggers.com/five-ways-to-visualize-your-pairwise-comparisons/ I've updated to remove warnings and errors.
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# originally from: | |
# http://groups.google.com/group/ggplot2/attach/6bf632a9718dddd6/ggcorplot.R?part=2 | |
# linked to from here: | |
# http://www.r-bloggers.com/five-ways-to-visualize-your-pairwise-comparisons/ | |
# I've updated to remove warnings and errors. | |
library(ggplot2) | |
#define a helper function (borrowed from the "ez" package) | |
ezLev=function(x,new_order){ | |
for(i in rev(new_order)){ | |
x=relevel(x,ref=i) | |
} | |
return(x) | |
} | |
ggcorplot = function(data,var_text_size,cor_text_limits){ | |
# normalize data | |
for(i in 1:length(data)){ | |
data[,i]=(data[,i]-mean(data[,i]))/sd(data[,i]) | |
} | |
# obtain new data frame | |
z=data.frame() | |
i = 1 | |
j = i | |
while(i<=length(data)){ | |
if(j>length(data)){ | |
i=i+1 | |
j=i | |
}else{ | |
x = data[,i] | |
y = data[,j] | |
temp=as.data.frame(cbind(x,y)) | |
temp=cbind(temp,names(data)[i],names(data)[j]) | |
z=rbind(z,temp) | |
j=j+1 | |
} | |
} | |
names(z)=c('x','y','x_lab','y_lab') | |
z$x_lab = ezLev(factor(z$x_lab),names(data)) | |
z$y_lab = ezLev(factor(z$y_lab),names(data)) | |
z=z[z$x_lab!=z$y_lab,] | |
#obtain correlation values | |
z_cor = data.frame() | |
i = 1 | |
j = i | |
while(i<=length(data)){ | |
if(j>length(data)){ | |
i=i+1 | |
j=i | |
}else{ | |
x = data[,i] | |
y = data[,j] | |
x_mid = min(x)+diff(range(x))/2 | |
y_mid = min(y)+diff(range(y))/2 | |
this_cor = cor(x,y) | |
this_cor.test = cor.test(x,y) | |
this_col = ifelse(this_cor.test$p.value<.05,'<.05','>.05') | |
this_size = (this_cor)^2 | |
cor_text = ifelse( | |
this_cor>0 | |
,substr(format(c(this_cor,.123456789),digits=2)[1],2,4) | |
,paste('-',substr(format(c(this_cor,.123456789),digits=2)[1],3,5),sep='') | |
) | |
b=as.data.frame(cor_text) | |
b=cbind(b,x_mid,y_mid,this_col,this_size,names(data)[j],names(data)[i]) | |
z_cor=rbind(z_cor,b) | |
j=j+1 | |
} | |
} | |
names(z_cor)=c('cor','x_mid','y_mid','p','rsq','x_lab','y_lab') | |
z_cor$x_lab = ezLev(factor(z_cor$x_lab),names(data)) | |
z_cor$y_lab = ezLev(factor(z_cor$y_lab),names(data)) | |
diag = z_cor[z_cor$x_lab==z_cor$y_lab,] | |
z_cor=z_cor[z_cor$x_lab!=z_cor$y_lab,] | |
#start creating layers | |
points_layer = layer( | |
geom = 'point' | |
, data = z | |
, mapping = aes( | |
x = x | |
, y = y | |
) | |
) | |
lm_line_layer = layer( | |
geom = 'line' | |
, geom_params = list(colour = 'red') | |
, stat = 'smooth' | |
, stat_params = list(method = 'lm') | |
, data = z | |
, mapping = aes( | |
x = x | |
, y = y | |
) | |
) | |
lm_ribbon_layer = layer( | |
geom = 'ribbon' | |
, geom_params = list(fill = 'green', alpha = .5) | |
, stat = 'smooth' | |
, stat_params = list(method = 'lm') | |
, data = z | |
, mapping = aes( | |
x = x | |
, y = y | |
) | |
) | |
cor_text = layer( | |
geom = 'text' | |
, data = z_cor | |
, mapping = aes( | |
x=y_mid | |
, y=x_mid | |
, label=cor | |
, size = rsq | |
, colour = p | |
) | |
) | |
var_text = layer( | |
geom = 'text' | |
, geom_params = list(size=var_text_size) | |
, data = diag | |
, mapping = aes( | |
x=y_mid | |
, y=x_mid | |
, label=x_lab | |
) | |
) | |
f = facet_grid(y_lab~x_lab,scales='free') | |
o = theme( | |
panel.grid.minor = element_blank() | |
,panel.grid.major = element_blank() | |
,axis.ticks = element_blank() | |
,axis.text.y = element_blank() | |
,axis.text.x = element_blank() | |
,axis.title.y = element_blank() | |
,axis.title.x = element_blank() | |
,legend.position='none' | |
) | |
size_scale = scale_size(limits = c(0,1),range=cor_text_limits) | |
return( | |
ggplot()+ | |
points_layer+ | |
lm_ribbon_layer+ | |
lm_line_layer+ | |
var_text+ | |
cor_text+ | |
f+ | |
o+ | |
size_scale | |
) | |
} | |
#set up some fake data | |
library(MASS) | |
N=100 | |
#first pair of variables | |
variance1=1 | |
variance2=2 | |
mean1=10 | |
mean2=20 | |
rho = .8 | |
Sigma=matrix(c(variance1,sqrt(variance1*variance2)*rho,sqrt(variance1*variance2)*rho,variance2),2,2) | |
pair1=mvrnorm(N,c(mean1,mean2),Sigma,empirical=T) | |
#second pair of variables | |
variance1=10 | |
variance2=20 | |
mean1=100 | |
mean2=200 | |
rho = -.4 | |
Sigma=matrix(c(variance1,sqrt(variance1*variance2)*rho,sqrt(variance1*variance2)*rho,variance2),2,2) | |
pair2=mvrnorm(N,c(mean1,mean2),Sigma,empirical=T) | |
my_data=data.frame(cbind(pair1,pair2)) | |
ggcorplot( | |
data = my_data | |
, var_text_size = 30 | |
, cor_text_limits = c(2,30) | |
) | |
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