README.R

#' ## Installation: 
# devtools::install_github("jakeyeung/SleepDepAnalysis")
# note: data objects can also be found in URL: https://zenodo.org/record/4057008
# There is an object called "dat_combat_countsfilt.5.5.Robj" that is >100 MB, which exceeds github hard limit.
# In GetCountsMatrix() the function downloads the .Robj from zenodo and loads it. 


# Jake Yeung
# Date of Creation: 2019-11-28
# File: ~/projects/SleepDepAnalysis/R/README.R
# Make a nice README.md for people to see how to plot the data



library(here)  # for loading Mara output, which needs to point to a directory
setwd(here())

library(hash)
library(reshape2)
library(dplyr)
library(Matrix)
library(ggplot2)
library(Rcpp)
library(SleepDepAnalysis)

suppressWarnings(suppressMessages(LoadPrimetimeObjs()))  # loads the processed data into R
act.zscore.lst <- LoadMaraOutput(act.dir = "data/sleep_deprivation_gene_exprs_all")  # function needs to point to directory

#' ## Explore the sleep deprivation data

#' The expression dynamics of many genes can be accurately predicted from sleep-wake history of mice:

g <- "Egr2"
print(PlotBestFit(subset(dat.long.shift, gene == g), subset(fits, gene == g), filt.time, g, wake.collapsed, low.pass.filt.time, dat.pred = NA, dat.eeg = dat.eeg.plot, jsize = 10))


#' Interestingly, clock and clock output genes were affected by sleep deprivation, often in a non-trivial manner:

g <- "Nr1d1"
print(PlotBestFit(subset(dat.long.shift, gene == g), subset(fits, gene == g), filt.time, g, wake.collapsed, low.pass.filt.time, dat.pred = NA, dat.eeg = dat.eeg.plot, jsize = 10))


#' We used a model selection to infer genes that may be sleep-wake driven, here's how to do the fits:

g <- "Egr2"

# HALF LIFE LIMITS
min.hl <- 1/3
max.hl <- 24
min.hl.mrna <- 1/3
max.hl.mrna <- 24

lambda <- 1000
jmaxiter <- 3000

jtswitch <- 33
jform <- "switch"

fit.output <- subset(dat.long.shift, gene == g) %>%
  group_by(gene) %>%
  do(fit.sleep = FitProcessS(., wake.collapsed, exprs.cname = "exprs", time.cname = "time",
                             condensed=TRUE, pseudo = 0, min.hl = min.hl, max.hl = max.hl,
                             do.lowpass=TRUE, min.hl.mrna = min.hl.mrna, max.hl.mrna = max.hl.mrna,
                             low.pass.filter.times = low.pass.filt.time, jlambda = lambda, jmaxit = jmaxiter),
     fit.flat = FitFlat(., use.weights = FALSE, get.bic = TRUE, condensed = TRUE),
     fit.circadian = FitRhythmic(., T.period = 24, use.weights=FALSE, get.bic=TRUE, condensed=TRUE),
     fit.ampfree.step = FitRhythmic.FreeAmp(., AmpFunc = AmpFunc, T.period = 24, tswitch = jtswitch, form = jform, include.intercept = TRUE, jmaxit = jmaxiter),
     fit.mixedaf = FitWeightedSFreeAmp(., AmpFunc = AmpFunc, wake.collapsed = wake.collapsed,
                                       exprs.cname = "exprs", time.cname = "time", T.period = 24,
                                       tswitch=jtswitch, form=jform, pseudo = 0, min.hl = min.hl,
                                       max.hl = max.hl, include.intercept = FALSE, do.lowpass=TRUE,
                                       min.hl.mrna = min.hl.mrna, max.hl.mrna = max.hl.mrna,
                                       low.pass.filter.times = low.pass.filt.time, jlambda = lambda, jmaxit = jmaxiter),
     fit.mix = FitWeightedSCircadian(., wake.collapsed, condensed = TRUE, pseudo = 0,
                                     min.hl = min.hl, max.hl = max.hl, include.mix.weight = FALSE,
                                     include.intercept = FALSE, do.lowpass=TRUE, min.hl.mrna = min.hl.mrna,
                                     max.hl.mrna = max.hl.mrna, low.pass.filter.times = low.pass.filt.time, jlambda = lambda, jmaxit = jmaxiter))
fit.output <- AddBICToDat(fit.output)
fit.output$model <- SelectBestModel(fit.output, colnames(fit.output))  # Egr2 is sleep-wake driven gene


#' We inferred regulators underlying the dynamics of many of these genes
#'

act.long <- act.zscore.lst$act.long
zscores <- act.zscore.lst$zscores
zscores$motif <- factor(as.character(zscores$motif), levels = zscores$motif)
zscores$label <- mapply(function(m, z) ifelse(z > 1.46, m, NA), as.character(zscores$motif), zscores$zscore)

#' We inferred that SRF may be driving many of the early-response dynamics
jmotif <- "SRF.p3"
act.means <- act.long %>%
  group_by(gene, time) %>%
  summarise(exprs = mean(exprs), sem = sqrt(sum(sem ^ 2)))
PlotMara.withEEG(subset(act.means, gene == jmotif), dat.eeg.plot, jtitle = jmotif, labsize = 10, ysize = 10)