## ----setup, echo=FALSE, results="hide"------------------------------------------------------------
knitr::opts_chunk$set(
  tidy = FALSE, 
  cache = TRUE,
  fig.align = 'center',
  dev = "png",
  package.startup.message = FALSE,
  message = FALSE, 
  error = FALSE, 
  warning = TRUE
)
options(width = 100)

## ----simResult, cache=TRUE, fig.height=4, fig.width=4---------------------------------------------
# load library
library("variancePartition")

# load simulated data:
# geneExpr: matrix of gene expression values
# info: information/metadata about each sample
data(varPartData)

# Specify variables to consider
# Age is continuous so model it as a fixed effect
# Individual and Tissue are both categorical,
# so model them as random effects
# Note the syntax used to specify random effects
form <- ~ Age + (1 | Individual) + (1 | Tissue) + (1 | Batch)

# Fit model and extract results
# 1) fit linear mixed model on gene expression
# If categorical variables are specified,
#     a linear mixed model is used
# If all variables are modeled as fixed effects,
# 		a linear model is used
# each entry in results is a regression model fit on a single gene
# 2) extract variance fractions from each model fit
# for each gene, returns fraction of variation attributable
# 		to each variable
# Interpretation: the variance explained by each variables
# after correcting for all other variables
# Note that geneExpr can either be a matrix,
# and EList output by voom() in the limma package,
# or an ExpressionSet
varPart <- fitExtractVarPartModel(geneExpr, form, info)

# sort variables (i.e. columns) by median fraction
# 		of variance explained
vp <- sortCols(varPart)

# Figure 1a
# Bar plot of variance fractions for the first 10 genes
plotPercentBars(vp[1:10, ])

# Figure 1b
# violin plot of contribution of each variable to total variance
plotVarPart(vp)

## ----accessResults, cache=TRUE, warning=FALSE-----------------------------------------------------
# Access first entries
head(varPart)

# Access first entries for Individual
head(varPart$Individual)

# sort genes based on variance explained by Individual
head(varPart[order(varPart$Individual, decreasing = TRUE), ])

## ----savePlot, cache=TRUE, eval=FALSE-------------------------------------------------------------
# fig <- plotVarPart(vp)
# ggsave(file, fig)

## ----plotStratify, cache=TRUE, warning=FALSE, fig.height=4, fig.width=4---------------------------
# get gene with the highest variation across Tissues
# create data.frame with expression of gene i and Tissue
# 		type for each sample
i <- which.max(varPart$Tissue)
GE <- data.frame(Expression = geneExpr[i, ], Tissue = info$Tissue)

# Figure 2a
# plot expression stratified by Tissue
plotStratify(Expression ~ Tissue, GE, main = rownames(geneExpr)[i])

# get gene with the highest variation across Individuals
# create data.frame with expression of gene i and Tissue
# 		type for each sample
i <- which.max(varPart$Individual)
GE <- data.frame(
  Expression = geneExpr[i, ],
  Individual = info$Individual
)

# Figure 2b
# plot expression stratified by Tissue
label <- paste("Individual:", format(varPart$Individual[i] * 100,
  digits = 3
), "%")
main <- rownames(geneExpr)[i]
plotStratify(Expression ~ Individual, GE,
  colorBy = NULL,
  text = label, main = main
)

## ----cache=TRUE-----------------------------------------------------------------------------------
library("lme4")

# fit regression model for the first gene
form_test <- geneExpr[1, ] ~ Age + (1 | Individual) + (1 | Tissue)
fit <- lmer(form_test, info, REML = FALSE)

# extract variance statistics
calcVarPart(fit)

## ----canCorPairs, cache=TRUE, results='hide', fig.width=5, fig.height=5---------------------------
form <- ~ Individual + Tissue + Batch + Age + Height

# Compute Canonical Correlation Analysis (CCA)
# between all pairs of variables
# returns absolute correlation value
C <- canCorPairs(form, info)

# Plot correlation matrix
# between all pairs of variables
plotCorrMatrix(C)

## ----simResult-omit, cache=TRUE, results='hide'---------------------------------------------------
form <- ~ Age + (1 | Individual) + (1 | Tissue) + (1 | Batch)

# Fit model
results <- fitVarPartModel(geneExpr, form, info)

# Extract results
varPart <- extractVarPart(results)

## ----simResult-fast-two-step, cache=TRUE, results='hide'------------------------------------------
# Fit model and run summary() function on each model fit
vpSummaries <- fitVarPartModel(geneExpr, form, info, fxn = summary)

## ----simResult-fast-two-step1, cache=TRUE---------------------------------------------------------
# Show results of summary() for the first gene
vpSummaries[[1]]

## ----vpa1, echo=TRUE, cache=TRUE, results='hide'--------------------------------------------------
form <- ~ (1 | Tissue) + (1 | Individual) + (1 | Batch) + Age
varPart <- fitExtractVarPartModel(geneExpr, form, info)

## ----vpa2, echo=TRUE, cache=TRUE, results='hide'--------------------------------------------------
library("limma")
# subtract out effect of Batch
fit <- lmFit(geneExpr, model.matrix(~Batch, info))
res <- residuals(fit, geneExpr)

# fit model on residuals
form <- ~ (1 | Tissue) + (1 | Individual) + Age

varPartResid <- fitExtractVarPartModel(res, form, info)

## ----vpa3, echo=TRUE, cache=TRUE, results='hide'--------------------------------------------------
# subtract out effect of Batch with linear mixed model
modelFit <- fitVarPartModel(geneExpr, ~ (1 | Batch), info)
res <- residuals(modelFit)

# fit model on residuals
form <- ~ (1 | Tissue) + (1 | Individual) + Age

varPartResid <- fitExtractVarPartModel(res, form, info)

## ----vpa4, echo=TRUE, cache=TRUE, results='hide'--------------------------------------------------
# extract residuals directly without storing intermediate results
residList <- fitVarPartModel(geneExpr, ~ (1 | Batch), info,
  fxn = residuals
)

# convert list to matrix
residMatrix <- do.call(rbind, residList)

## ----withinTissue, echo=TRUE, cache=TRUE, results='hide', fig.height=5, fig.width=4---------------
# specify formula to model within/between individual variance
# separately for each tissue
# Note that including +0 ensures each tissue is modeled explicitly
# Otherwise, the first tissue would be used as baseline
form <- ~ (Tissue + 0 | Individual) + Age + (1 | Tissue) + (1 | Batch)

# fit model and extract variance percents
varPart <- fitExtractVarPartModel(geneExpr, form, info, showWarnings = FALSE)

# violin plot
plotVarPart(sortCols(varPart), label.angle = 60)

## ----echo=TRUE, cache=TRUE, results='hide'--------------------------------------------------------
form <- ~ (1 | Individual) + (1 | Tissue) + Age + Height

# fit model
res <- fitVarPartModel(geneExpr[1:4, ], form, info)

## ----echo=TRUE, cache=TRUE------------------------------------------------------------------------
# evaluate the collinearity score on the first model fit
# this reports the correlation matrix between coefficient estimates
# for fixed effects
# the collinearity score is the maximum absolute correlation value
# If the collinearity score > .99 then the variance partition
# estimates may be problematic
# In that case, a least one variable should be omitted
colinearityScore(res[[1]])

## ----echo=TRUE, cache=TRUE, results='hide'--------------------------------------------------------
form <- ~ (1 | Individual) + (1 | Tissue) + Age + Height

# Specify custom weights
# In this example the weights are simulated from a
# uniform distribution and are not meaningful.
weights <- matrix(runif(length(geneExpr)), nrow = nrow(geneExpr))

# Specify custom weights
res <- fitExtractVarPartModel(geneExpr[1:4, ], form, info,
  weightsMatrix = weights[1:4, ]
)

## ----vpInteraction, echo=TRUE, cache=TRUE, results='hide', fig.width=4, fig.height=4--------------
form <- ~ (1 | Individual) + Age + Height + (1 | Tissue) + (1 | Batch) +
  (1 | Batch:Tissue)

# fit model
vpInteraction <- fitExtractVarPartModel(geneExpr, form, info)

plotVarPart(sortCols(vpInteraction))

## ----limma, echo=TRUE, cache=TRUE, results='hide'-------------------------------------------------
library("limma")
library("edgeR")

# identify genes that pass expression cutoff
isexpr <- rowSums(cpm(geneCounts) > 1) >= 0.5 * ncol(geneCounts)

# create data structure with only expressed genes
gExpr <- DGEList(counts = geneCounts[isexpr, ])

# Perform TMM normalization
gExpr <- calcNormFactors(gExpr)

# Specify variables to be included in the voom() estimates of
# uncertainty.
# Recommend including variables with a small number of categories
# that explain a substantial amount of variation
design <- model.matrix(~Batch, info)

# Estimate precision weights for each gene and sample
# This models uncertainty in expression measurements
vobjGenes <- voom(gExpr, design)

# Define formula
form <- ~ (1 | Individual) + (1 | Tissue) + (1 | Batch) + Age

# variancePartition seamlessly deals with the result of voom()
# by default, it seamlessly models the precision weights
# This can be turned off with useWeights=FALSE
varPart <- fitExtractVarPartModel(vobjGenes, form, info)

## ----DESeq2, echo=TRUE, cache=TRUE, results='hide'------------------------------------------------
library("DESeq2")

# create DESeq2 object from gene-level counts and metadata
dds <- DESeqDataSetFromMatrix(
  countData = geneCounts,
  colData = info,
  design = ~1
)

# Estimate library size correction scaling factors
dds <- estimateSizeFactors(dds)

# identify genes that pass expression cutoff
isexpr <- rowSums(fpm(dds) > 1) >= 0.5 * ncol(dds)

# compute log2 Fragments Per Million
# Alternatively, fpkm(), vst() or rlog() could be used
quantLog <- log2(fpm(dds)[isexpr, ] + 1)

# Define formula
form <- ~ (1 | Individual) + (1 | Tissue) + (1 | Batch) + Age

# Run variancePartition analysis
varPart <- fitExtractVarPartModel(quantLog, form, info)

## ----tximport, echo=TRUE, cache=TRUE, results='hide', eval=FALSE----------------------------------
# library("tximportData")
# library("tximport")
# library("readr")
# 
# # Get data from folder where tximportData is installed
# dir <- system.file("extdata", package = "tximportData")
# samples <- read.table(file.path(dir, "samples.txt"), header = TRUE)
# files <- file.path(dir, "kallisto", samples$run, "abundance.tsv")
# names(files) <- paste0("sample", 1:6)
# 
# tx2gene <- read.csv(file.path(dir, "tx2gene.csv"))
# 
# # reads results from kallisto
# txi <- tximport(files,
#   type = "kallisto", tx2gene = tx2gene,
#   countsFromAbundance = "lengthScaledTPM"
# )
# 
# # define metadata (usually read from external source)
# info_tximport <- data.frame(
#   Sample = sprintf("sample%d", 1:6),
#   Disease = c("case", "control")[c(rep(1, 3), rep(2, 3))]
# )
# 
# # Extract counts from kallisto
# y <- DGEList(txi$counts)
# 
# # compute library size normalization
# y <- calcNormFactors(y)
# 
# # apply voom to estimate precision weights
# design <- model.matrix(~Disease, data = info_tximport)
# vobj <- voom(y, design)
# 
# # define formula
# form <- ~ (1 | Disease)
# 
# # Run variancePartition analysis (on only 10 genes)
# varPart_tx <- fitExtractVarPartModel(
#   vobj[1:10, ], form,
#   info_tximport
# )

## ----ballgown, echo=TRUE, cache=TRUE, results='hide'----------------------------------------------
library("ballgown")

# Get data from folder where ballgown is installed
data_directory <- system.file("extdata", package = "ballgown")

# Load results of Cufflinks/Tablemaker
bg <- ballgown(
  dataDir = data_directory, samplePattern = "sample",
  meas = "all"
)

# extract gene-level FPKM quantification
# Expression can be convert to log2-scale if desired
gene_expression <- gexpr(bg)

# extract transcript-level FPKM quantification
# Expression can be convert to log2-scale if desired
transcript_fpkm <- texpr(bg, "FPKM")

# define metadata (usually read from external source)
info_ballgown <- data.frame(
  Sample = sprintf("sample%02d", 1:20),
  Batch = rep(letters[1:4], 5),
  Disease = c("case", "control")[c(rep(1, 10), rep(2, 10))]
)

# define formula
form <- ~ (1 | Batch) + (1 | Disease)

# Run variancePartition analysis
# Gene-level analysis
varPart_gene <- fitExtractVarPartModel(
  gene_expression, form,
  info_ballgown
)

# Transcript-level analysis
varPart_transcript <- fitExtractVarPartModel(
  transcript_fpkm, form,
  info_ballgown
)

## ----sim, echo=FALSE, cache=TRUE, results='hide'--------------------------------------------------
library("variancePartition")

sim_data <- function(n, p, var_indiv, var_site) {
  info <- data.frame(
    ID = paste("s", 1:n, sep = ""),
    Individual = factor(rep(round(seq(1, n / 6, length.out = n / 6)), 6)),
    Tissue = factor(sort(rep(toupper(letters[1:3]), n / 3))),
    Age = rpois(n, 50)
  )

  geneExpr <- matrix(0, nrow = p, ncol = n)
  for (i in 1:p) {
    beta_indiv <- rnorm(nlevels(info$Individual), 0, sqrt(var_indiv))
    beta_site <- rnorm(nlevels(info$Tissue), 0, sqrt(var_site))
    eta <- model.matrix(~Individual, info) %*% beta_indiv + model.matrix(~ Tissue + 0, info) %*% beta_site

    noise <- rbeta(1, 10, 100)
    errVar <- var(eta) * (noise) / (1 - noise)

    geneExpr[i, ] <- eta + rnorm(n, 0, sqrt(errVar))
  }
  colnames(geneExpr) <- paste("s", 1:ncol(geneExpr), sep = "")
  rownames(geneExpr) <- paste("gene", 1:nrow(geneExpr), sep = "")

  return(list(info = info, geneExpr = geneExpr))
}

plotVar <- function(geneExpr, info) {
  form <- ~ (1 | Individual) + (1 | Tissue)
  varPart <- suppressWarnings(fitExtractVarPartModel(geneExpr, form, info, showWarnings=FALSE))
  plotVarPart(varPart, col = c(rainbow(8)[1:2], "grey85")) + theme(aspect.ratio=1)
}

plotVarCross <- function(geneExpr, info, label.angle = 30) {
  form <- ~ (Tissue + 0 | Individual) + (1 | Tissue)

  # res = fitVarPartModel( geneExpr, form, info )
  # varPart = extractVarPart( res )

  varPart <- suppressWarnings(fitExtractVarPartModel(geneExpr, form, info, showWarnings = FALSE))

  plotVarPart(varPart, label.angle = label.angle) + theme(aspect.ratio=1)
}

plotPCA <- function(geneExpr, col, main='') {
  dcmp <- prcomp(t(geneExpr))

  par(mar = c(4, 4, 1, 1) + 0.1)
  plot(dcmp$x[, 1:2], col = col, main=main)
}

plotTree <- function(geneExpr, col, main=main) {
  hc <- hclust(dist(t(geneExpr)))
  library("dendextend")
  hcd <- as.dendrogram(hc)
  labels_colors(hcd) <- col[match(labels(hcd), names(col))]

  par(mar = c(4, 4, 1, 1) + 0.1, cex = .6)
  plot(hcd, yaxt = "n", horiz = TRUE, main=main)
}

## ----siteDominant, echo=FALSE, fig.height=8, fig.width=8, fig.show="hold", warnings=TRUE----------
set.seed(1)

n <- 60
p <- 200  

data <- sim_data(n, p, 1, 4)

colTissue <- rainbow(nlevels(data$info$Tissue))[data$info$Tissue]
names(colTissue) <- data$info$ID

colIndiv <- rainbow(nlevels(data$info$Individual))[data$info$Individual]
names(colIndiv) <- data$info$ID

par(mfrow=c(2,2))
plotPCA(data$geneExpr, colTissue, main = "(a) PCA - colored by Tissue")

plotPCA(data$geneExpr, colIndiv, main = "(b) PCA - colored by Individual") 

plotTree(data$geneExpr, colTissue, main ="(c) hclust - colored by Tissue")
legend("topleft", legend = levels(data$info$Tissue), fill = rainbow(nlevels(data$info$Tissue))[1:nlevels(data$info$Tissue)], title = "Tissue")

plotTree(data$geneExpr, colIndiv, main="(d) hclust - colored by Individual")
legend("topleft", legend = levels(data$info$Individual), fill = rainbow(nlevels(data$info$Individual))[1:nlevels(data$info$Individual)], title = "Individual")


## ----cowplot, echo=FALSE, fig.width=8-------------------------------------------------------------
fig1 = plotVar(data$geneExpr, data$info)
fig2 = plotVarCross(data$geneExpr, data$info, label.angle = 60)

cowplot::plot_grid(fig1 + ggtitle("Variance partitioning"), fig2 + ggtitle("variancePartition - within Tissue"), axis="tblr", align="hv")

## ----IndivDominant, echo=FALSE, fig.height=8, fig.width=8-----------------------------------------
set.seed(1)

n <- 60
p <- 200

data <- sim_data(n, p, 3, 1)

colTissue <- rainbow(nlevels(data$info$Tissue))[data$info$Tissue]
names(colTissue) <- data$info$ID

colIndiv <- rainbow(nlevels(data$info$Individual))[data$info$Individual]
names(colIndiv) <- data$info$ID

par(mfrow=c(2,2))
plotPCA(data$geneExpr, colTissue, main = "(a) PCA - colored by Tissue")

plotPCA(data$geneExpr, colIndiv, main = "(b) PCA - colored by Individual") 

plotTree(data$geneExpr, colTissue, main ="(c) hclust - colored by Tissue")
legend("topleft", legend = levels(data$info$Tissue), fill = rainbow(nlevels(data$info$Tissue))[1:nlevels(data$info$Tissue)], title = "Tissue")

plotTree(data$geneExpr, colIndiv, main="(d) hclust - colored by Individual")
legend("topleft", legend = levels(data$info$Individual), fill = rainbow(nlevels(data$info$Individual))[1:nlevels(data$info$Individual)], title = "Individual")


## ----cowplot2, echo=FALSE, fig.width=8------------------------------------------------------------
fig1 = plotVar(data$geneExpr, data$info)
fig2 = plotVarCross(data$geneExpr, data$info, label.angle = 60)

cowplot::plot_grid(fig1 + ggtitle("Variance partitioning"), fig2 + ggtitle("variancePartition - within Tissue"), axis="tblr", align="hv")

## ----stop, echo=FALSE, cache=FALSE----------------------------------------------------------------
# if( "cluster" %in% class(cl) ){
if (exists("cl")) {
  library("doParallel")

  # stop cluster and catch warning if invalid
  res <- tryCatch({
    stopCluster(cl)
  }, warning = function(x) {
  }, error = function(x) {
  }, finally = {
  })
  # warning("STOP CLUSTER!!!!!!!!!!!!!!!!!\n")
}

## ----DE, echo=FALSE, cache=TRUE, fig.height=5, fig.width=8, warnings=FALSE------------------------
set.seed(1)

library("variancePartition")

n <- 500
data <- data.frame(Sex = factor(c(rep("F", n), rep("M", n))))
data$expression <- rnorm(2 * n, (as.integer(data$Sex) - 1) * 2, .3)
data$Sex <- factor(data$Sex)

fit <- lm(expression ~ Sex, data)
# calcVarPart(fit)
# coef(fit)[2]

fig1 = plotStratify(expression ~ Sex, data, ylim = c(-6, 9)) +
  annotate("text", x = 0.5, y = 9, hjust = 0, label = paste("fold change:", format(coef(fit)[2], digits = 3)), size = 5.5) +
  annotate("text", x = 0.5, y = 8, hjust = 0, label = paste("% variance of expression:", format(calcVarPart(fit)[1] * 100, digits = 3), "%"), size = 5.5) + ggtitle("Example A")


n <- 500
data <- data.frame(Sex = factor(c(rep("F", n), rep("M", n))))
data$expression <- rnorm(2 * n, (as.integer(data$Sex) - 1) * 2, 2.01)
data$Sex <- factor(data$Sex)

fit <- lm(expression ~ Sex, data)
# calcVarPart(fit)
# coef(fit)[2]

fig2 = plotStratify(expression ~ Sex, data, ylim = c(-6.6, 9)) +
  annotate("text", x = 0.5, y = 9, hjust = 0, label = paste("fold change:", format(coef(fit)[2], digits = 3)), size = 5.5) +
  annotate("text", x = 0.5, y = 8, hjust = 0, label = paste("% variance of expression:", format(calcVarPart(fit)[1] * 100, digits = 3), "%"), size = 5.5) + ggtitle("Example B")

cowplot::plot_grid(fig1 + theme(aspect.ratio=1), fig2+ theme(aspect.ratio=1))

## ----session, echo=FALSE--------------------------------------------------------------------------
sessionInfo()

