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## ----setup, echo=FALSE, results="hide"-----------------------------------
knitr::opts_chunk$set(comment = "#>", collapse = TRUE)
## ---- eval = FALSE-------------------------------------------------------
# install.packages("LPWC")
## ---- eval = FALSE-------------------------------------------------------
# devtools::install_github("gitter-lab/LPWC@vx.xx.x")
# #OR
# devtools::install_version("LPWC", version = "x.x.x", repos = "http://cran.us.r-project.org")
## ---- eval = FALSE-------------------------------------------------------
# devtools::install_github("gitter-lab/LPWC")
## ----lib, results="asis", eval=TRUE--------------------------------------
library(LPWC)
## ----data, results='markup'----------------------------------------------
data(simdata)
simdata[1:5, ]
str(simdata)
## ----time----------------------------------------------------------------
timepoints <- c(0, 2, 4, 6, 8, 18, 24, 32, 48, 72)
timepoints
## ---- echo = FALSE, fig.height = 2, fig.width=4, warning = FALSE, fig.align='center'----
library(ggplot2)
set.seed(29876)
a <- rbind(c(rep(0, 5), 8, 0), c(rep(0, 4), 4.3, 0, 0)) + rnorm(2, 0, 0.5)
dat <- data.frame(intensity = as.vector(a), time = rep(c(0, 5, 15, 30, 45, 60, 75), each = 2), genes = factor(rep(c(1, 2), 7)))
a2 <- a
a2[1, ] <- c(a2[1, 2:7], NA)
dat2 <- data.frame(intensity = as.vector(a2), time = rep(c(0, 5, 15, 30, 45, 60, 75), each = 2), genes = factor(rep(c(1, 2), 7)))
a3 <- a
a3[2, ] <- c(NA, a3[2, 1:6])
a3[1, ] <- c(a3[1, 2:7], NA)
dat3 <- data.frame(intensity = as.vector(a3), time = rep(c(0, 5, 15, 30, 45, 60, 75), each = 2), genes = factor(rep(c(1, 2), 7)))
plot1 <- ggplot(dat, aes(x= time, y = intensity, group = genes)) + geom_line(aes(color = genes), size = 1.5) + labs(x = "Time (min)") + labs(y = "Intensity")
plot1
row1 <- c(0, 5, 15, 30, 45, 60, 75)
knitr::kable(t(data.frame(Original = row1, Gene1 = row1, Gene2 = row1)), align = 'c')
## ---- echo = FALSE, fig.height = 2, fig.width=4, warning = FALSE, fig.align='center'----
plot2 <- ggplot(dat2, aes(x= time, y = intensity, group = genes)) + geom_line(aes(color = genes), size = 1.5) +
labs(x = "Time (min)") + labs(y = "Intensity")
plot2
row2 <- c(5, 15, 30, 45, 60, 75, "-")
knitr::kable(t(data.frame(Original = row1, Gene1 = row2, Gene2 = row1)), align = 'c')
## ---- echo = FALSE, fig.height = 2, fig.width=4, warning = FALSE, fig.align='center'----
plot3 <- ggplot(dat3, aes(x= time, y = intensity, group = genes)) + geom_line(aes(color = genes), size = 1.5) +
labs(x = "Time (min)") + labs(y = "Intensity")
plot3
row3 <- c("-", 0, 5, 15, 30, 45, 60)
knitr::kable(t(data.frame(Original = row1, Gene1 = row2, Gene2 = row3)), align = 'c')
## ------------------------------------------------------------------------
LPWC::corr.bestlag(simdata[49:58, ], timepoints = timepoints, max.lag = 2, penalty = "high", iter = 10)
## ----clust1, fig.width=5-------------------------------------------------
dist <- 1 - LPWC::corr.bestlag(simdata[11:20, ], timepoints = timepoints, max.lag = 2, penalty = "low", iter = 10)$corr
plot(hclust(dist))
## ----clust 2-------------------------------------------------------------
dist <- 1 - LPWC::corr.bestlag(simdata[11:20, ], timepoints = timepoints, max.lag = 2, penalty = "low", iter = 10)$corr
cutree(hclust(dist), k = 3)
## ---- eval = FALSE-------------------------------------------------------
# indexnon0 <- apply(data, 1, function(x){which(var(x) != 0)})
# subset.data <- data[indexnon0, ]
## ----sessionInfo---------------------------------------------------------
sessionInfo()
## ---- eval = FALSE-------------------------------------------------------
#
#
# # This function stores two different list separately
# comb <- function(x, ...) {
# lapply(seq_along(x),
# function(i) c(x[[i]], lapply(list(...), function(y) y[[i]])))
# }
#
#
# # adding the data
# data <- simdata[1:10, ]
# # number of iterations
# iter <- 10
# # C values that are used in the algorithm
# allC <- findC(timepoints = timepoints, iter = iter)
#
# # setting the clusters
# core <- parallel::detectCores() - 1
# cl <- parallel::makeCluster(core)
#
# # assigning the parallelization
# doParallel::registerDoParallel(cl)
#
#
# ## running the algorithm for different C
# result <- foreach(i = 1:iter, .combine='comb', .multicombine=TRUE,
# .init=list(list(), list())) %dopar% {
# lags <- best.lag(data, max.lag = 3, timepoints = timepoints, C = allC[i])
# new.data <- prep.data(data = data, lags = lags, timepoints = timepoints)
# corr <- comp.corr(new.data$data, new.data$time, C = allC[i])
# return(list(corr, lags))
# }
#
#
# # dividing the list into two different list: one for lags and one for all the correlations
# allcorr <- result[[1]]
# alllags <- result[[2]]
#
# # picking best C
# val <- rep(NA, (length(iter) - 1))
# for(i in 1:(iter - 1)){
# val[i] <- sum((as.vector(allcorr[[i + 1]]) - as.vector(allcorr[[i]]))^2)
# }
#
# # returning the results for the best C
# result <- list(corr = allcorr[[which.min(val) + 1]], lags = alllags[[which.min(val) + 1]], C = values[which.min(val) + 1])
#
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