--- a
+++ b/Examples/dtw_example.R
@@ -0,0 +1,35 @@
+# An example to run DTW time delay analysis across modalities.
+
+library(tidyverse)
+library(dtw)
+library(zoo)
+
+gene = 'EGR1'
+bins = 20
+
+# input file contains three columns: latent time, motif accessibility, and TF gene expression
+res = read.delim(paste0(gene, '_res.txt'), sep=' ', header = F, stringsAsFactors = F)
+colnames(res) = c('t', 'm', 'r')
+res = res[order(res$t),]
+
+res$t = res$t * bins
+res$window = floor(res$t / 1)
+res$window[res$window==bins] = bins-1
+res2 = aggregate(res, by=list(res$window), FUN=mean)
+
+rv = res2$r - min(res2$r)
+rv = c(rv[1], rv, rv[length(rv)])
+rv = rollmean(rv, 3)
+rv[1] = 0
+rv[length(rv)] = 0
+rv = rv / max(rv)
+mv = res2$m - min(res2$m)
+mv = c(mv[1], mv, mv[length(mv)])
+mv = rollmean(mv, 3)
+mv[1] = 0
+mv[length(mv)] = 0
+mv = mv / max(mv)
+
+# compute dtw
+dtw.res = dtw(rv, mv, keep.internals = T)
+dtwPlotTwoWay(dtw.res, col=c('magenta', '#f7ba41'), lwd=3, xlab='latent time', ylab='accessibility and expression')