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File S14.R
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File S14.R
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#=============================================================================================================#
# Script created by Jennifer C Molloy, [email protected]
# Script created in version R 3.1.2
# This script is for analyzing and displaying data related to the Molloy et al. paper describing
# Wolbachia modulation of lipid metabolism in Aedes albopictus mosquito cells
# Datasets can be found at http://www.ebi.ac.uk/metabolights/MTBLS210
#=============================================================================================================#
# Set working directory
setwd("/home/jenny/Dropbox/LipidPaper/")
#clear R environment
rm(list=ls())
library("plyr")
library("lattice")
library("ggplot2")
library("reshape2")
library("extrafont")
library("stringr")
library("dplyr")
library("cairoDevice")
library("matrixStats")
library("scales")
library("grid")
load(fonts)
#=============================================================================================================#
##################### Predefine necessary functions for plotting #####################################
#=============================================================================================================#
## Function for arranging ggplots. use png(); arrange(p1, p2, ncol=1); dev.off() to save.
### From Stephen Turner via http://www.gettinggeneticsdone.com/2010/03/arrange-multiple-ggplot2-plots-in-same.html
vp.layout <- function(x, y) viewport(layout.pos.row=x, layout.pos.col=y)
arrange_ggplot2 <- function(..., nrow=NULL, ncol=NULL, as.table=FALSE) {
dots <- list(...)
n <- length(dots)
if(is.null(nrow) & is.null(ncol)) { nrow = floor(n/2) ; ncol = ceiling(n/nrow)}
if(is.null(nrow)) { nrow = ceiling(n/ncol)}
if(is.null(ncol)) { ncol = ceiling(n/nrow)}
## NOTE see n2mfrow in grDevices for possible alternative
grid.newpage()
pushViewport(viewport(layout=grid.layout(nrow,ncol) ) )
ii.p <- 1
for(ii.row in seq(1, nrow)){
ii.table.row <- ii.row
if(as.table) {ii.table.row <- nrow - ii.table.row + 1}
for(ii.col in seq(1, ncol)){
ii.table <- ii.p
if(ii.p > n) break
print(dots[[ii.table]], vp=vp.layout(ii.table.row, ii.col))
ii.p <- ii.p + 1
}
}
}
# Need to display fold-change in lipid abundance with the y-intercept at 1 (no change)
# so remove -1 to 1 in the axis as these are redundant values.
# Function scaleBreaker "takes a chunk" out of the series
# written by dsparks and available from https://gist.github.com/dsparks/4086721#file-rcp_plot-r
scaleBreaker <- function(x, mn, mx){
y <- x # ^ vector, low end, high end
y[x > mn & x < mx] <- mn
y[x >= mx] <- x[x >= mx] - mx + mn
return(y)
}
# Make it into a scale breaking between -1 and 1, with the package scales
break_trans = function() trans_new("break", # min v v max
function(x) scaleBreaker(x, -1, 1),
function(x) x)
#=============================================================================================================#
################# COUNT DATA FOR FOLD-CHANGE #########################
#=============================================================================================================#
# import data from file S16 Table saved as a csv
full.lcms <- read.csv("/home/jenny/Dropbox/LipidPaper/Test/S16\ Table.csv",
sep=",",
header=TRUE,
stringsAsFactors = FALSE,
skip=17
)
head(full.lcms)
#Split lcms$Annotation.note into lipid class, carbon chain length and saturation using regular expressions
lcms <- subset(full.lcms, grepl("^(\\w+\\-?\\w+)\\s([1-9][0-9]):([0-9])", Annotation.note)) #select rows containing annotation
matches <- str_match(lcms$Annotation.note,"^(\\w+\\-?\\w+)\\s([1-9][0-9]):([0-9])")
lcms.annotation <- data.frame(na.omit(matches[,-1]),stringsAsFactors=FALSE) # transform to data frame
colnames(lcms.annotation) <- c("Class","Chain","Saturation") # add a header
lcms.annotation$Chain <- as.integer(lcms.annotation$Chain) # convert type of chain length from character to integer
lcms.annotation$Saturation <- as.integer(lcms.annotation$Saturation) # convert type of saturation from character to integer
#Bind lcms.annotation data to lcms
lcms <- cbind(lcms,lcms.annotation)
# Make a table with numbers of species in each class that:
# "-|-" = Decrease in both wMel and wMelPop infection with q.value < 0.05
# "+|+" = Increase in both wMel and wMelPop infection with q.value < 0.05
# "+|-" = Increase in wMel and decrease in wMelPop with q.value < 0.05
# "-|+" = Increase in wMelPop and decrease in wMel with q.value < 0.05
# "None" = No significant changes in either infection with q.value < 0.05
ddply(lcms,.(Class),
summarise,
"-|-" = length(Class[q.value < 0.05 & Change.A.to.AM < 1 & Change.A.to.AP < 1]),
"+|+" = length(Class[q.value < 0.05 & Change.A.to.AM > 1 & Change.A.to.AP > 1]),
"+|-" = length(Class[q.value < 0.05 & Change.A.to.AM > 1 & Change.A.to.AP < 1]),
"-|+" = length(Class[q.value < 0.05 & Change.A.to.AM < 1 & Change.A.to.AP > 1]),
"None" = length(Class[q.value > 0.05]),
"Total" = length(Class)
)
#=============================================================================================================#
################### MEAN FOLD-CHANGE DATA PLOTS #################################
#=============================================================================================================#
#Select only lipids manually annotated and flagged for plotting
#Load list of selected MZ values
plot.selection <- read.csv("/home/jenny/Dropbox/LipidPaper/Test/manual-plotting-selection.csv",
sep=",",
header=TRUE,
stringsAsFactors = FALSE,
)
## Rename lcms$M.Z column to MZ
lcms <- rename(lcms, MZ = M.Z)
## Select only lipid species in manually curated list
lcms.subset <- subset(lcms, MZ %in% plot.selection$MZ)
#Convert change ratios to fold change and bind new column
lcms.subset <- lcms.subset %>%
mutate(wMel.foldchange = ifelse(Change.A.to.AM<1,
(-(1/Change.A.to.AM)),
Change.A.to.AM)) %>%
mutate(wMelPop.foldchange = ifelse(Change.A.to.AP<1,
(-(1/Change.A.to.AP)),
Change.A.to.AP))
# make vectors of value and variable names
lcms.names <- (names(lcms))
lcms.valuenames <- c("wMel.foldchange","wMelPop.foldchange")
lcms.variablenames <- lcms.names[! lcms.names %in% lcms.valuenames]
#Melt dataset
lcms.full.long <- melt(lcms.subset, id=lcms.variablenames)
str(lcms.full.long)
glimpse(lcms.full.long)
#Define lipid class categories for plotting and select only significant changes (q.value < 0.05)
## Only plotting [M+Hac-H]- ions for Cer so remove all other ions
lcms.long.cer <- filter(lcms.full.long, Class == "Cer" & Ion.form == "[M+Hac-H]-" & q.value < 0.05)
## Only plotting [M-H]- ions for HexCer so remove all other ions
lcms.long.hexcer <- filter(lcms.full.long, Class == "HexCer" & Ion.form == "[M-H]-" & q.value < 0.05)
## Only plotting [M+Hac-H]- ions for LacCer so remove all other ions
lcms.long.laccer <- filter(lcms.full.long, Class == "LacCer" & Ion.form == "[M+Hac-H]-" & q.value < 0.05)
## Only plotting [M-H]- ions for PE-Cer so remove all other ions
lcms.long.pecer <- filter(lcms.full.long, Class == "PE-Cer" & Ion.form == "[M-H]-" & q.value < 0.05)
## Only plotting [M+Hac-H]- ions for SM so remove all other ions
lcms.long.sm <- filter(lcms.full.long, Class == "SM" & Ion.form == "[M+Hac-H]-" & q.value < 0.05)
## Only plotting [M+Hac-H]- ions for DG so remove all other ions
lcms.long.dg <- filter(lcms.full.long, Class == "DG" & Ion.form == "[M+Hac-H]-" & q.value < 0.05)
## Only plotting [M+Hac-H]- ions for PC so remove all other ions
lcms.long.pc <- filter(lcms.full.long, Class == "PC" & Ion.form == "[M+Hac-H]-" & q.value < 0.05)
## Only plotting [M+Hac-H]- ions for LPC so remove all other ions
lcms.long.lpc <- filter(lcms.full.long, Class == "LPC" & Ion.form == "[M+Hac-H]-" & q.value < 0.05)
## Only plotting [M-H]- ions for PE so remove all other ions
lcms.long.pe <- filter(lcms.full.long, Class == "PE" & Ion.form == "[M-H]-" & q.value < 0.05)
## Only plotting [M-H]- ions for LPE so remove all other ions
lcms.long.lpe <- filter(lcms.full.long, Class == "LPE" & Ion.form == "[M-H]-" & q.value < 0.05)
## Only plotting [M-H]- ions for PG so remove all other ions
lcms.long.pg <- filter(lcms.full.long, Class == "PG" & Ion.form == "[M-H]-" & q.value < 0.05)
## Only plotting [M-H]- ions for PI so remove all other ions
lcms.long.pi <- filter(lcms.full.long, Class == "PI" & Ion.form == "[M-H]-" & q.value < 0.05)
## Too few PS per ion form to filter on this
lcms.long.ps <- filter(lcms.full.long, Class == "PS" & q.value < 0.05)
lcms.long <- rbind(lcms.long.cer,
lcms.long.hexcer,
lcms.long.pecer,
lcms.long.sm,
lcms.long.dg,
lcms.long.pc,
lcms.long.lpc,
lcms.long.pe,
lcms.long.pg,
lcms.long.pi,
lcms.long.ps )
# LacCer and LPE not included due to lack of values (only five datapoints)
## Set lipid class groups to enable grouping of data by class in graphs
cer.class <- c("Cer","HexCer","PE-Cer","SM")
phospho.class <- c("PS","PI","PG","PE","PC","PA", "LPC")
fa.class <- c("DG","TG")
#Subset long dataset by class groups
lipid.class.cer <- subset(lcms.long , Class %in% cer.class)
lipid.class.phospho <- subset(lcms.long , Class %in% phospho.class)
lipid.class.fa <- subset(lcms.long , Class %in% fa.class)
glimpse(lipid.class.cer)
#=============================================================================================================#
############ MEAN FOLD-CHANGE CALCULATIONS ############################
#=============================================================================================================#
# Calculate table of mean raw ratio change in cell lines by lipid class
ratio.change <- function(x){c(
mean.ratio.wMel<- mean(x$Change.A.to.AM),
mean.ratio.wMelPop <- mean(x$Change.A.to.AP))
cbind(mean.ratio.wMel,mean.ratio.wMelPop)}
ratio.change.byclass <- ddply(lcms, c("Class"),function(df)ratio.change(df))
#=============================================================================================================#
####### SPHINGOLIPIDS FOLD-CHANGE PLOTS##############
#=============================================================================================================#
#Plot mean fold-change per sphingolipid class
## Pre-define y axis breaks and labels
cer.breaks <- myLabels <- c(-12:-2, 1, 2:8)
cer.plot <- ggplot(lipid.class.cer , aes(x = Class,
y = value,
fill=variable)) +
scale_fill_manual(values=c("#999999", "#CCCCCC"),
labels=c("Aa23.wMel", "Aa23.wMelPop"))+
geom_boxplot(outlier.size = 0) +
geom_point(position = position_jitterdodge(jitter.width = 0.2,
jitter.height = 0,
dodge.width = 0.75),
alpha=0.6,
pch=19)+
# format axes
scale_y_continuous(breaks = cer.breaks)+
coord_trans(y = "break")+ # Apply custom scale
geom_hline(yintercept=1, linetype="dotted", size=1)+
xlab("Sphingolipid Subclass")+
ylab("Mean fold-change compared to Aa23-T")+
# format legend and theme
guides(fill=guide_legend(title=NULL))+
theme_bw(base_size = 14)+
theme(legend.justification=c(1,0),
legend.position=c(1,0),
axis.title.x = element_text(vjust=-0.5),
axis.title.y = element_text(vjust=0.9),
legend.background = element_rect(fill="transparent"))
cer.plot
#=============================================================================================================#
####### PHOSPHOLIPIDS FOLD-CHANGE PLOTS ##############
#=============================================================================================================#
#Plot mean fold-change per phospholipid class
phospho.breaks <- myLabels <- c(-7:-2, 1, 2:5)
phospho.plot <- ggplot(lipid.class.phospho , aes(x = Class,
y = value,
fill=variable)) +
scale_fill_manual(values=c("#999999", "#CCCCCC"),
labels=c("Aa23.wMel", "Aa23.wMelPop"))+
geom_boxplot(outlier.size = 0) +
geom_point(position = position_jitterdodge(jitter.width = 0.2,
jitter.height = 0,
dodge.width = 0.75),
alpha=0.6,
pch=19)+
# format axes
scale_y_continuous(breaks = cer.breaks)+
coord_trans(y = "break")+ # Apply custom scale
geom_hline(yintercept=0, linetype="dotted", size=1)+
xlab("Phospholipid Subclass")+
ylab("Mean fold-change compared to Aa23-T")+
guides(fill=guide_legend(title=NULL))+
theme_bw(base_size = 14)+
theme(legend.justification=c(0,1),
legend.position=c(0,1),
axis.title.x = element_text(vjust=-0.5),
axis.title.y = element_text(vjust=0.9),
legend.background = element_rect(fill="transparent"))
phospho.plot
#=============================================================================================================#
####### FATTY ACIDS FOLD-CHANGE PLOTS ##############
#=============================================================================================================#
#Plot mean fold-change per FA class
phospho.breaks <- myLabels <- c(-6:-2, 1, 2:4)
fa.plot <- ggplot(lipid.class.fa , aes(x = Class,
y = value,
fill=variable)) +
scale_fill_manual(values=c("#999999", "#CCCCCC"),
labels=c("Aa23.wMel", "Aa23.wMelPop"))+
geom_boxplot(outlier.size = 0) +
geom_point(position = position_jitterdodge(jitter.width = 0.2,
jitter.height = 0,
dodge.width = 0.75),
alpha=0.6,
pch=19)+
# format axes
scale_y_continuous(breaks = cer.breaks)+
coord_trans(y = "break")+ # Apply custom scale
geom_hline(yintercept=0, linetype="dotted", size=1)+
ylab("Mean fold-change compared to Aa23-T")+
guides(fill=guide_legend(title=NULL))+
theme_bw(base_size = 14)+
theme(legend.justification=c(0,1),
legend.position=c(0,0.3),
axis.title.x = element_text(vjust=-0.5),
axis.title.y = element_text(vjust=0.9),
legend.background = element_rect(fill="transparent"))
fa.plot
#=============================================================================================================#
############ DETAILED FOLD-CHANGE PLOTS BY CHAIN LENGTH AND SATURATION ######################
#=============================================================================================================#
############ Ceramides ############
cer.detailed.breaks <- myLabels <- c(-12:-2, 1, 2:4)
cer.detailed.plot <- ggplot( subset(lipid.class.cer, Class == "Cer" & Saturation < 3),
#use Cer class only and ignore polyunsaturated lipids with >2 double bonds (only one species)
aes(x = as.factor(Chain), #make the x axis categorical
y = value,
fill=variable,
width=0.75)) +
facet_grid(~Saturation
,scales = "free_x"
)+ #free scales so no gaps along x-axis
scale_fill_manual(values=c("#4D4D4D", "#CCCCCC"),
labels=c("Aa23.wMel", "Aa23.wMelPop"))+
geom_bar(stat="identity", position="dodge")+
# format axes
scale_y_continuous(breaks = cer.detailed.breaks)+
coord_trans(y = "break")+ # Apply custom scale
geom_hline(yintercept=0, size=0.5)+
ylab("Mean fold-change compared to Aa23-T")+
xlab("Carbon Chain Length")+
guides(fill=guide_legend(title=NULL))+
theme_bw(base_size = 12, base_family = "sans")+
theme(legend.justification=c(0,1),
legend.position=c(0,0.2),
axis.title.x = element_text(vjust=-0.5),
axis.title.y = element_text(vjust=0.9),
legend.background = element_rect(fill="transparent"),
strip.text.x = element_text(size=12, face="bold"))
cer.detailed.plot
############ DGs ############
dg.detailed.breaks <- myLabels <- c(-6:-2, 1, 2:4)
dg.detailed.plot <- ggplot(lipid.class.fa,
#use Cer class only and ignore polyunsaturated lipids with >2 double bonds (only one species)
aes(x = as.factor(Chain), #make the x axis catergorical
y = value,
fill=variable,
width=0.75)) +
facet_grid(~Saturation, scales = "free_x")+ #free scales so no gaps along x-axis
scale_fill_manual(values=c("#4D4D4D", "#CCCCCC"),
labels=c("Aa23.wMel", "Aa23.wMelPop"))+
geom_bar(stat="identity", position="dodge")+
# format axes
scale_y_continuous(breaks = dg.detailed.breaks)+
coord_trans(y = "break")+ # Apply custom scale
geom_hline(yintercept=0, size=0.5)+
ylab("Mean fold-change compared to Aa23-T")+
xlab("Carbon Chain Length")+
guides(fill=guide_legend(title=NULL))+
theme_bw(base_size = 12, base_family = "sans")+
theme(legend.justification=c(0,0.75),
legend.position=c(0.75,0.3),
axis.title.x = element_text(vjust=-0.5),
axis.title.y = element_text(vjust=0.9),
legend.background = element_rect(fill="transparent"),
strip.text.x = element_text(size=12, face="bold"))
dg.detailed.plot
############ PCs by saturation and chain length ############
pc.chain.detailed.breaks <- myLabels <- c(-5:-2, 1, 2:4)
pc.chain.detailed.plot <- ggplot(subset(lipid.class.phospho, Class == "PC"& Saturation < 3),
aes(x = as.factor(Chain), #make the x axis catergorical
y = value,
fill=variable,
width=0.75)) +
facet_grid(~Saturation, scales = "free_x")+ #free scales so no gaps along x-axis
scale_fill_manual(values=c("#4D4D4D", "#CCCCCC"),
labels=c("Aa23.wMel", "Aa23.wMelPop"))+
geom_bar(stat="identity", position="dodge")+
# format axes
scale_y_continuous(breaks = pc.chain.detailed.breaks)+
coord_trans(y = "break")+ # Apply custom scale
geom_hline(yintercept=0, size=0.5)+
ylab("Mean fold-change compared to Aa23-T")+
xlab("Carbon Chain Length")+
ggtitle("A) PC fold-change by chain length")+
guides(fill=guide_legend(title=NULL))+
theme_bw(base_size = 12, base_family = "sans")+
theme(legend.justification=c(0,1),
legend.position=c(0.75,0.3),
plot.title = element_text(vjust=0.9, size=14, face="bold"),
axis.title.x = element_text(vjust=-0.5),
axis.title.y = element_text(vjust=0.9),
legend.background = element_rect(fill="transparent"),
strip.text.x = element_text(size=12, face="bold"))
pc.chain.detailed.plot
pc.saturation.detailed.breaks <- myLabels <- c(-5:-2, 1, 2:4)
pc.saturation.detailed.plot <- ggplot(subset(lipid.class.phospho, Class == "PC" & Chain %in% c("36","38","40")),
aes(x = as.factor(Saturation), #make the x axis catergorical
y = value,
fill=variable,
width=0.75)) +
facet_grid(~Chain, scales = "free_x")+ #free scales so no gaps along x-axis
scale_fill_manual(values=c("#4D4D4D", "#CCCCCC"),
labels=c("Aa23.wMel", "Aa23.wMelPop"))+
geom_bar(stat="identity", position="dodge")+
# format axes
scale_y_continuous(breaks = pc.saturation.detailed.breaks)+
coord_trans(y = "break")+ # Apply custom scale
geom_hline(yintercept=0, size=0.5)+
ylab("Mean fold-change compared to Aa23-T")+
xlab("Number of double bonds")+
ggtitle("B) PC fold-change by saturation")+
guides(fill=guide_legend(title=NULL))+
theme_bw(base_size = 12, base_family = "sans")+
scale_y_continuous(breaks=scales::pretty_breaks(n = 10))+
theme(legend.position = "none",
plot.title = element_text(vjust=0.9, size=14, face="bold"),
axis.title.x = element_text(vjust=-0.5),
axis.title.y = element_text(vjust=0.9),
legend.background = element_rect(fill="transparent"),
strip.text.x = element_text(size=12, face="bold"))
pc.saturation.detailed.plot
pc.detailed.plot <- arrange_ggplot2(pc.chain.detailed.plot, pc.saturation.detailed.plot, ncol=1)
############ PEs by saturation and chain length ############
pe.saturation <- c(0,1,2,3,4) #set vector of saturations levels to include
pe.saturation.detailed.breaks <- myLabels <- c(-5:-2, 1, 2:5)
pe.detailed.plot <- ggplot(subset(lipid.class.phospho, Class == "PE" & Saturation %in% pe.saturation),
aes(x = as.factor(Chain), #make the x axis catergorical
y = value,
fill=variable,
width=0.75)) +
facet_grid(~Saturation, scales = "free_x")+ #free scales so no gaps along x-axis
scale_fill_manual(values=c("#4D4D4D", "#CCCCCC"),
labels=c("Aa23.wMel", "Aa23.wMelPop"))+
geom_bar(stat="identity", position="dodge")+
# format axes
scale_y_continuous(breaks = pe.saturation.detailed.breaks)+
coord_trans(y = "break")+ # Apply custom scale
geom_hline(yintercept=0,size=0.5)+
ylab("Mean fold-change compared to Aa23-T")+
xlab("Carbon Chain Length")+
guides(fill=guide_legend(title=NULL))+
theme_bw(base_size = 14, base_family = "sans")+
theme(legend.justification=c(0,1),
legend.position=c(0.8,1),
axis.title.x = element_text(vjust=-0.5),
axis.title.y = element_text(vjust=0.9),
legend.background = element_rect(fill="transparent"),
strip.text.x = element_text(size=12, face="bold"))
pe.detailed.plot
#=============================================================================================================#
############# COMBINE FOLD-CHANGE AND INTENSITY DATASETS #################
#=============================================================================================================#
# Read in normalised matrix of signal intensities from LCMS
# available from http://www.ebi.ac.uk/metabolights/MTBLS210
normmatrix <- t(read.table("/home/jenny/Dropbox/LipidPaper/Tables/TableS4.csv",
sep=",",
check.names = TRUE))
# Add MZ column label and remove unecessary rows
normmatrix[1,1]="MZ"
normmatrix<- normmatrix[-c(2:3),]
head(normmatrix)
# Take column names from first row then delete
colnames(normmatrix) <- normmatrix[1,]
normmatrix<- (normmatrix)[-1,]
normdata <- as.data.frame(normmatrix)
# Subset for experimental samples
normdata.Aa23 <- normdata[,1:20]
head(normdata.Aa23 )
#create column of numbers 1:number of experimental samples
id <- c(1:ncol(normdata.Aa23))
# Change factors to numeric in those columns
normdata.Aa23[,id] <- as.numeric(as.character(unlist(normdata.Aa23[,id])))
# Create a Peak column and add the ID number list
normdata.Aa23$Peak = c(1:nrow(normdata.Aa23))
# Prepare to merge datasets by MZ values
## Round up MZ in lcms dataset to 3 d.p for merging (otherwise unable to match MZ index columns)
lcms$MZ = round(lcms$MZ, digits=3)
## Merge LCMS annotations and normalised intensity matrix
lcms.merged <- join(lcms, normdata.Aa23, by="MZ", type = "inner")
#=============================================================================================================#
########### Plot mean intensities per treatment per species #############
#=============================================================================================================#
## Define column names for each treatment type: Aa23T, Aa23TwMel and Aa23TwMelPop
Aa23T.names <- c("A1","A2","A3","A4","A5","A6")
Aa23TwMel.names <- c("B1","B2","B3","B4","B5","B6")
Aa23TwMelPop.names <- c("C1","C2","C3","C4","C5","C6")
lcms.merged.selection <- subset(lcms.merged, select = c("MZ","INTENSITY",Aa23T.names,Aa23TwMel.names,Aa23TwMelPop.names))
Aa23T.selection <- subset(lcms.merged, select = Aa23T.names)
Aa23TwMel.selection <- subset(lcms.merged, select = Aa23TwMel.names)
Aa23TwMelPop.selection <- subset(lcms.merged, select = Aa23TwMelPop.names)
## Calculate mean per treatment per signal and add as additional column
lcms.merged$Aa23T.mean <- rowMeans(Aa23T.selection, na.rm = TRUE)
lcms.merged$Aa23TwMel.mean <- rowMeans(Aa23TwMel.selection, na.rm = TRUE)
lcms.merged$Aa23TwMelPop.mean <- rowMeans(Aa23TwMelPop.selection, na.rm = TRUE)
# Subset the four columns of interest: "MZ", "Class", "Aa23T.mean", "Aa23TwMel.mean", "Aa23TwMelPop.mean"
# from the lcms.merged dataset
lcms.merged.means <-(subset(lcms.merged,
select = c("MZ",
"Class",
"Aa23T.mean",
"Aa23TwMel.mean",
"Aa23TwMelPop.mean")))
# Melt lcms.merged.means into long format ready to feed into ggplot
lcms.merged.means.long <- melt(lcms.merged.means, id.vars=c("MZ", "Class"))
head(lcms.merged.means.long)
# Plot the mean intensity for each signal by lipid class and treatment
# Used a boxplot to show distribution, not much meaning added by including all points
# Tried reducing ymax but no real change to message and many outliers not displayed
intensity.boxplot <-
ggplot(lcms.merged.means.long, aes(x = Class,
y = value,
fill=variable))+
geom_boxplot(pch=19)+
scale_fill_manual(values=c("white", "#999999", "#CCCCCC"),
labels=c("Aa23-T", "Aa23.wMel", "Aa23.wMelPop"))+
xlab("Lipid Class")+
ylab("Mean Intensity")+
ylim(0,350000000)+
guides(fill=guide_legend(title=NULL))+
theme_bw(base_size = 12,
base_family = "sans")+
theme(legend.justification=c(0,1),
legend.position=c(0,1),
axis.title.x = element_text(vjust=-0.5),
axis.title.y = element_text(vjust=0.9),
legend.background = element_rect(fill="transparent"))
intensity.boxplot
#=============================================================================================================#
###### SAVE PLOTS TO FILE ################
#=============================================================================================================#
cairo_ps("/home/jenny/Dropbox/LipidPaper/fig3.eps",
width = 4,
height = 5,
family = "sans")
cer.plot
dev.off()
postscript("/home/jenny/Dropbox/LipidPaper/S17_fig.eps",
width = 8,
height = 5,
horizontal = FALSE,
onefile = FALSE,
paper = "special",
colormodel = "rgb",
family = "sans")
cer.detailed.plot
dev.off()
cairo_ps("/home/jenny/Dropbox/LipidPaper/fig5.eps",
width = 3,
height = 5,
family = "sans")
fa.plot
dev.off()
postscript("/home/jenny/Dropbox/LipidPaper/S18_fig.eps",
width = 8,
height = 5,
horizontal = FALSE,
onefile = FALSE,
paper = "special",
colormodel = "rgb",
family = "sans")
dg.detailed.plot
dev.off()
cairo_ps("/home/jenny/Dropbox/LipidPaper/fig6.eps",
width = 6,
height = 5,
family = "sans")
phospho.plot
dev.off()
postscript("/home/jenny/Dropbox/LipidPaper/S19_fig.eps",
width = 8,
height = 10,
horizontal = FALSE,
onefile = FALSE,
paper = "special",
colormodel = "rgb",
family = "sans")
arrange_ggplot2(pc.chain.detailed.plot, pc.saturation.detailed.plot, ncol=1)
dev.off()
postscript("/home/jenny/Dropbox/LipidPaper/S21_fig.eps",
width = 10,
height = 5,
horizontal = FALSE,
onefile = FALSE,
paper = "special",
colormodel = "rgb",
family = "sans")
intensity.boxplot
dev.off()
postscript("/home/jenny/Dropbox/LipidPaper/S20_fig.eps",
width = 10,
height = 5,
horizontal = FALSE,
onefile = FALSE,
paper = "special",
colormodel = "rgb",
family = "sans")
pe.detailed.plot
dev.off()