spaghetti plots

spag.R

# construct spaghetti plots in R
# skip to the last few lines for the actual ggplot definition
#
# melt to long format
# in this case, we have subjects with a dv collected 
#   1) at multiple timepoints (wave)
#   2) in multiple brain regions (region)
# subjects also have an age, which helps make a prettier spaghetti plot
require(reshape2)
long_data <- melt(wide_data, id.vars=c("ID", "wave", "age"))
names(long_data) <- c("ID", "wave", "age", "region", "dv")
long_data$ID <- factor(long_data$ID)

# long_data should at this point have (subjects * waves * regions) rows

# calcuate the delta for each person
# this is only used to colorize the segments (i.e., use color to show slope)
# so skip if you don't need it
# recast back to wide, by waves
wide_data_delta <- dcast(long_data, ID+region~wave, value.var="dv")
wide_data_delta$delta <- wide_data_delta[["2"]] - wide_data_delta[["1"]]
long_data <- merge(long_data, subset(wide_data_delta, select=c("ID", "region", "delta")), by=c("ID", "region"))

# plot
require(ggplot2)
q <- ggplot(long_data, aes(x=age, y=dv, group=ID, colour=delta)) + 
  geom_line() + 
  geom_point() +
  facet_wrap(~region) + theme_bw() + scale_colour_gradient2(low="green", high="red", mid="darkblue")
print(q)