Miami plots
email title: "help with Miami plots" - from Carolina
May 25th 2021
Embedded Files
Location on server: /space/chen-syn01/1/data/cinliu/plots/miami
/space/chen-syn01/1/data/cinliu/plots/miami/mami
/space/chen-syn01/1/data/cinliu/plots/miami/mami.zip
The top half of the Miami plots: /space/chen-syn01/1/data/cmakowski/GWASgclus_UKB/Mar2020_fastGWA/phenotypes/main_analysis/sumstats/*fastGWA
The bottom half of the Miami: /space/chen-syn01/1/data/cmakowski/GWASgclus_UKB/Mar2020_fastGWA/phenotypes/noglobals/sumstats/*fastGWA
miami_odd_only.R
#! /usr/bin/env Rscript
rm(list=ls())library(data.table)library(ggplot2)
Path <- "/Users/nini/Desktop/2021lab/carolina/"setwd(Path)
######################################### # point towards sumstats and set params ##########################################
# ls *3103*area*fastGWA > ChenSumstatsArea.txt# ls *3103*thick*fastGWA > ChenSumstatsThick.txt#data on server #The top half of the Miami plots: /space/chen-syn01/1/data/cmakowski/GWASgclus_UKB/Mar2020_fastGWA/phenotypes/main_analysis/sumstats/*fastGWA#The bottom half of the Miami: /space/chen-syn01/1/data/cmakowski/GWASgclus_UKB/Mar2020_fastGWA/phenotypes/noglobals/sumstats/*fastGWA
FileNames <- fread("/Users/nini/Desktop/2021lab/carolina/area_mmil_features.txt",data.table=F,header = F)FileNames$V2 <- gsub("UKB39k_Chen_GWAS_DM_310320_ChenA_bh_","",FileNames$V1)Sets <- gsub("_area_sumstat.fastGWA","",FileNames$V2)for(i in 1:length(Sets)){
dat1 <- fread(paste0("/Users/nini/Desktop/2021lab/carolina/top/UKB39k_Chen_GWAS_DM_310320_",Sets[i],"_sumstat.fastGWA"),data.table=F)[,c("CHR","POS","P")] dat2 <- fread(paste0("/Users/nini/Desktop/2021lab/carolina/bottom/UKB39k_Chen_GWAS_DM_060420_",Sets[i],"_sumstat.fastGWA"),data.table=F)[,c("CHR","POS","P")] topcols <- c("grey72","grey42") botcols <- c("grey72","grey42") pcutoff <- 0.2 # cut away SNPs with P above this value, removing most SNPs, so it runs faster. ############### # Prep inputs # ############### colnames(dat1) <- c("chr","pos","p") -> colnames(dat2) dat1 <- dat1[complete.cases(dat1),] dat2 <- dat2[complete.cases(dat2),] ###### Create df with chr positions chrmaxpos <- data.frame("chr"=1:22,"maxpos"=NA,"genomestartpos"=NA) for(j in 1:22){ chrmaxpos$maxpos[j] <- max(c(dat1$pos[dat1$chr==j],dat2$pos[dat2$chr==j])) if(j==1){chrmaxpos$genomestartpos[j] <- 0 } else { chrmaxpos$genomestartpos[j] <- chrmaxpos$genomestartpos[j-1] + chrmaxpos$maxpos[j-1] } } ## label position chrmaxpos$labpos <- chrmaxpos$genomestartpos + 0.5*chrmaxpos$maxpos ####### Add genomic position to sumstats dat1$gpos <- NA -> dat2$gpos for(k in 1:22){ dat1$gpos[dat1$chr==k] <- dat1$pos[dat1$chr==k]+chrmaxpos$genomestartpos[k] dat2$gpos[dat2$chr==k] <- dat2$pos[dat2$chr==k]+chrmaxpos$genomestartpos[k] } ####### set graph parameters #maxp1 <- -log10(min(dat1$p)) #maxp2 <- -log10(min(dat2$p)) plotdat1 <- dat1[dat1$p<pcutoff,] plotdat2 <- dat2[dat2$p<pcutoff,] col1 <- rep(topcols,22)[plotdat1$chr] col2 <- rep(botcols,22)[plotdat2$chr] # if setting the y min as 20, if they pass 20 the y is set according to the max height of the indiviudal plot maxp1<- 20 maxp2<- 20 yAxisInterval <- 10 if (max(-log10(plotdat1$p))>20) { maxp1<- max(-log10(plotdat1$p))+0.5 yAxisInterval <- 20 } if ( max(-log10(plotdat2$p))>20) { maxp2<- max(-log10(plotdat2$p))+0.5 yAxisInterval <- 20 } if ( max(-log10(plotdat2$p))<25 | max(-log10(plotdat1$p))<25) { yAxisInterval <- 10 } axisLabNumTop <- ceiling(maxp1/yAxisInterval) # number of labels needed for each side of axis axisLabNumBottom <- ceiling(maxp2/yAxisInterval) axisLabAt <- c(seq(-yAxisInterval*axisLabNumBottom -4, -4,yAxisInterval),seq(4,yAxisInterval*(axisLabNumTop+1),yAxisInterval)) axisLabels <- c(seq(axisLabNumBottom*yAxisInterval,0,-yAxisInterval),0,seq(yAxisInterval,axisLabNumTop*yAxisInterval,yAxisInterval)) xlable <- c("1" , "", "3" ,"", "5" , "", "7" , "" , "9" , "" , "11", "", "13", "", "15", "","17", "" ,"19", "" ,"21" ,"")
Miami <- ggplot(plotdat1, aes(x=gpos, y=-log10(p)+4)) + theme_bw() + geom_hline(yintercept = -log10(5e-8)+4,color="navyblue",linetype="dashed",size=2) + geom_hline(yintercept = log10(5e-8)-4,color="navyblue",linetype="dashed",size=2) + geom_hline(yintercept = 4,color="black") + geom_hline(yintercept = -4,color="black") + geom_point(col=col1,size=3) + geom_point(data=plotdat2,aes(x=gpos,y=log10(p)-4),col=col2,inherit.aes = F, size=3) + scale_y_continuous(name="-log10(P-value) \n",limits=c(-maxp2-6, ifelse(maxp1<100,maxp1+6,110)),breaks=axisLabAt,labels = axisLabels) + geom_text(data=chrmaxpos,aes(x=labpos,y=0),label=as.character(1:22),size=4.5,inherit.aes = F) + expand_limits(y = 1) + # or some other arbitrarily large number #ggtitle(name1) + xlab(name2) + theme(plot.title=element_text(size=40,hjust = 0.5,margin = margin(b = -20),vjust = -6), axis.title.x=element_blank(), axis.text.x=element_blank(), axis.ticks.x=element_blank(), axis.title.y = element_text(size = 40,margin = margin(t = 0, r = -40, b = 0, l = 0)), axis.text.y = element_text(size = 40), panel.grid.minor = element_blank(), panel.grid.major = element_blank(), plot.background = element_blank(), #panel.border = element_blank(), plot.margin=unit(c(0.4,0,0.4,0.3),"cm"), #t,r,b,l panel.background = element_rect(colour = NA, fill = 'white')) ggsave(paste0(Path,"plots/normal/",Sets[i],"_AREA_MainvsNoGlob.png"), plot = Miami, width = 15, height = 7,bg="transparent") }
FileNames <- fread("/Users/nini/Desktop/2021lab/carolina/thickness_mmil_features.txt",data.table=F,header = F)FileNames$V2 <- gsub("UKB39k_Chen_GWAS_DM_310320_ChenT_bh_","",FileNames$V1)Sets <- gsub("_thickness_sumstat.fastGWA","",FileNames$V2)
for(i in 1:length(Sets)){ dat1 <- fread(paste0("/Users/nini/Desktop/2021lab/carolina/top/UKB39k_Chen_GWAS_DM_310320_",Sets[i],"_sumstat.fastGWA"),data.table=F)[,c("CHR","POS","P")] dat2 <- fread(paste0("/Users/nini/Desktop/2021lab/carolina/bottom/UKB39k_Chen_GWAS_DM_060420_",Sets[i],"_sumstat.fastGWA"),data.table=F)[,c("CHR","POS","P")] topcols <- c("grey72","grey42") botcols <- c("grey72","grey42") pcutoff <- 0.2 # cut away SNPs with P above this value, removing most SNPs, so it runs faster. ############### # Prep inputs # ############### colnames(dat1) <- c("chr","pos","p") -> colnames(dat2) dat1 <- dat1[complete.cases(dat1),] dat2 <- dat2[complete.cases(dat2),] ###### Create df with chr positions chrmaxpos <- data.frame("chr"=1:22,"maxpos"=NA,"genomestartpos"=NA) for(j in 1:22){ chrmaxpos$maxpos[j] <- max(c(dat1$pos[dat1$chr==j],dat2$pos[dat2$chr==j])) if(j==1){chrmaxpos$genomestartpos[j] <- 0 } else { chrmaxpos$genomestartpos[j] <- chrmaxpos$genomestartpos[j-1] + chrmaxpos$maxpos[j-1] } } ## label position chrmaxpos$labpos <- chrmaxpos$genomestartpos + 0.5*chrmaxpos$maxpos ####### Add genomic position to sumstats dat1$gpos <- NA -> dat2$gpos for(k in 1:22){ dat1$gpos[dat1$chr==k] <- dat1$pos[dat1$chr==k]+chrmaxpos$genomestartpos[k] dat2$gpos[dat2$chr==k] <- dat2$pos[dat2$chr==k]+chrmaxpos$genomestartpos[k] } ####### set graph parameters #maxp1 <- -log10(min(dat1$p)) #maxp2 <- -log10(min(dat2$p)) plotdat1 <- dat1[dat1$p<pcutoff,] plotdat2 <- dat2[dat2$p<pcutoff,] col1 <- rep(topcols,22)[plotdat1$chr] col2 <- rep(botcols,22)[plotdat2$chr] # if setting the y min as 20, if they pass 20 the y is set according to the max height of the indiviudal plot maxp1<- 20 maxp2<- 20 yAxisInterval <- 10 if (max(-log10(plotdat1$p))>20) { maxp1<- max(-log10(plotdat1$p))+0.5 yAxisInterval <- 20 } if ( max(-log10(plotdat2$p))>20) { maxp2<- max(-log10(plotdat2$p))+0.5 yAxisInterval <- 20 } if ( max(-log10(plotdat2$p))<25 | max(-log10(plotdat1$p))<25) { yAxisInterval <- 10 } axisLabNumTop <- ceiling(maxp1/yAxisInterval) # number of labels needed for each side of axis axisLabNumBottom <- ceiling(maxp2/yAxisInterval) axisLabAt <- c(seq(-yAxisInterval*axisLabNumBottom -4, -4,yAxisInterval),seq(4,yAxisInterval*(axisLabNumTop+1),yAxisInterval)) axisLabels <- c(seq(axisLabNumBottom*yAxisInterval,0,-yAxisInterval),0,seq(yAxisInterval,axisLabNumTop*yAxisInterval,yAxisInterval)) xlable <- c("1" , "", "3" ,"", "5" , "", "7" , "" , "9" , "" , "11", "", "13", "", "15", "","17", "" ,"19", "" ,"21" ,"")
Miami <- ggplot(plotdat1, aes(x=gpos, y=-log10(p)+4)) + theme_bw() + geom_hline(yintercept = -log10(5e-8)+4,color="navyblue",linetype="dashed",size=2) + geom_hline(yintercept = log10(5e-8)-4,color="navyblue",linetype="dashed",size=2) + geom_hline(yintercept = 4,color="black") + geom_hline(yintercept = -4,color="black") + geom_point(col=col1,size=3) + geom_point(data=plotdat2,aes(x=gpos,y=log10(p)-4),col=col2,inherit.aes = F, size=3) + scale_y_continuous(name="-log10(P-value) \n",limits=c(-maxp2-6, ifelse(maxp1<100,maxp1+6,110)),breaks=axisLabAt,labels = axisLabels) + geom_text(data=chrmaxpos,aes(x=labpos,y=0),label=as.character(1:22),size=4.5,inherit.aes = F) + expand_limits(y = 1) + # or some other arbitrarily large number #ggtitle(name1) + xlab(name2) + theme(plot.title=element_text(size=40,hjust = 0.5,margin = margin(b = -20),vjust = -6), axis.title.x=element_blank(), axis.text.x=element_blank(), axis.ticks.x=element_blank(), axis.title.y = element_text(size = 40,margin = margin(t = 0, r = -40, b = 0, l = 0)), axis.text.y = element_text(size = 40), panel.grid.minor = element_blank(), panel.grid.major = element_blank(), plot.background = element_blank(), #panel.border = element_blank(), plot.margin=unit(c(0.4,0,0.4,0.3),"cm"), #t,r,b,l panel.background = element_rect(colour = NA, fill = 'white')) ggsave(paste0(Path,"plots/normal/",Sets[i],"_THICKNESS_MainvsNoGlob.png"), plot = Miami, width = 15, height = 7,bg="transparent") }
rm(list=ls())library(data.table)library(ggplot2)
Path <- "/Users/nini/Desktop/2021lab/carolina/"setwd(Path)
######################################### # point towards sumstats and set params ##########################################
# ls *3103*area*fastGWA > ChenSumstatsArea.txt# ls *3103*thick*fastGWA > ChenSumstatsThick.txt#data on server #The top half of the Miami plots: /space/chen-syn01/1/data/cmakowski/GWASgclus_UKB/Mar2020_fastGWA/phenotypes/main_analysis/sumstats/*fastGWA#The bottom half of the Miami: /space/chen-syn01/1/data/cmakowski/GWASgclus_UKB/Mar2020_fastGWA/phenotypes/noglobals/sumstats/*fastGWA
FileNames <- fread("/Users/nini/Desktop/2021lab/carolina/area_mmil_features.txt",data.table=F,header = F)FileNames$V2 <- gsub("UKB39k_Chen_GWAS_DM_310320_ChenA_bh_","",FileNames$V1)Sets <- gsub("_area_sumstat.fastGWA","",FileNames$V2)for(i in 1:length(Sets)){
dat1 <- fread(paste0("/Users/nini/Desktop/2021lab/carolina/top/UKB39k_Chen_GWAS_DM_310320_",Sets[i],"_sumstat.fastGWA"),data.table=F)[,c("CHR","POS","P")] dat2 <- fread(paste0("/Users/nini/Desktop/2021lab/carolina/bottom/UKB39k_Chen_GWAS_DM_060420_",Sets[i],"_sumstat.fastGWA"),data.table=F)[,c("CHR","POS","P")] topcols <- c("grey72","grey42") botcols <- c("grey72","grey42") pcutoff <- 0.2 # cut away SNPs with P above this value, removing most SNPs, so it runs faster. ############### # Prep inputs # ############### colnames(dat1) <- c("chr","pos","p") -> colnames(dat2) dat1 <- dat1[complete.cases(dat1),] dat2 <- dat2[complete.cases(dat2),] ###### Create df with chr positions chrmaxpos <- data.frame("chr"=1:22,"maxpos"=NA,"genomestartpos"=NA) for(j in 1:22){ chrmaxpos$maxpos[j] <- max(c(dat1$pos[dat1$chr==j],dat2$pos[dat2$chr==j])) if(j==1){chrmaxpos$genomestartpos[j] <- 0 } else { chrmaxpos$genomestartpos[j] <- chrmaxpos$genomestartpos[j-1] + chrmaxpos$maxpos[j-1] } } ## label position chrmaxpos$labpos <- chrmaxpos$genomestartpos + 0.5*chrmaxpos$maxpos ####### Add genomic position to sumstats dat1$gpos <- NA -> dat2$gpos for(k in 1:22){ dat1$gpos[dat1$chr==k] <- dat1$pos[dat1$chr==k]+chrmaxpos$genomestartpos[k] dat2$gpos[dat2$chr==k] <- dat2$pos[dat2$chr==k]+chrmaxpos$genomestartpos[k] } ####### set graph parameters #maxp1 <- -log10(min(dat1$p)) #maxp2 <- -log10(min(dat2$p)) plotdat1 <- dat1[dat1$p<pcutoff,] plotdat2 <- dat2[dat2$p<pcutoff,] col1 <- rep(topcols,22)[plotdat1$chr] col2 <- rep(botcols,22)[plotdat2$chr] # if setting the y min as 20, if they pass 20 the y is set according to the max height of the indiviudal plot maxp1<- 20 maxp2<- 20 yAxisInterval <- 10 if (max(-log10(plotdat1$p))>20) { maxp1<- max(-log10(plotdat1$p))+0.5 yAxisInterval <- 20 } if ( max(-log10(plotdat2$p))>20) { maxp2<- max(-log10(plotdat2$p))+0.5 yAxisInterval <- 20 } if ( max(-log10(plotdat2$p))<25 | max(-log10(plotdat1$p))<25) { yAxisInterval <- 10 } axisLabNumTop <- ceiling(maxp1/yAxisInterval) # number of labels needed for each side of axis axisLabNumBottom <- ceiling(maxp2/yAxisInterval) axisLabAt <- c(seq(-yAxisInterval*axisLabNumBottom -4, -4,yAxisInterval),seq(4,yAxisInterval*(axisLabNumTop+1),yAxisInterval)) axisLabels <- c(seq(axisLabNumBottom*yAxisInterval,0,-yAxisInterval),0,seq(yAxisInterval,axisLabNumTop*yAxisInterval,yAxisInterval)) xlable <- c("1" , "", "3" ,"", "5" , "", "7" , "" , "9" , "" , "11", "", "13", "", "15", "","17", "" ,"19", "" ,"21" ,"")
Miami <- ggplot(plotdat1, aes(x=gpos, y=-log10(p)+4)) + theme_bw() + geom_hline(yintercept = -log10(5e-8)+4,color="navyblue",linetype="dashed",size=2) + geom_hline(yintercept = log10(5e-8)-4,color="navyblue",linetype="dashed",size=2) + geom_hline(yintercept = 4,color="black") + geom_hline(yintercept = -4,color="black") + geom_point(col=col1,size=3) + geom_point(data=plotdat2,aes(x=gpos,y=log10(p)-4),col=col2,inherit.aes = F, size=3) + scale_y_continuous(name="-log10(P-value) \n",limits=c(-maxp2-6, ifelse(maxp1<100,maxp1+6,110)),breaks=axisLabAt,labels = axisLabels) + geom_text(data=chrmaxpos,aes(x=labpos,y=0),label=as.character(1:22),size=4.5,inherit.aes = F) + expand_limits(y = 1) + # or some other arbitrarily large number #ggtitle(name1) + xlab(name2) + theme(plot.title=element_text(size=40,hjust = 0.5,margin = margin(b = -20),vjust = -6), axis.title.x=element_blank(), axis.text.x=element_blank(), axis.ticks.x=element_blank(), axis.title.y = element_text(size = 40,margin = margin(t = 0, r = -40, b = 0, l = 0)), axis.text.y = element_text(size = 40), panel.grid.minor = element_blank(), panel.grid.major = element_blank(), plot.background = element_blank(), #panel.border = element_blank(), plot.margin=unit(c(0.4,0,0.4,0.3),"cm"), #t,r,b,l panel.background = element_rect(colour = NA, fill = 'white')) ggsave(paste0(Path,"plots/normal/",Sets[i],"_AREA_MainvsNoGlob.png"), plot = Miami, width = 15, height = 7,bg="transparent") }
FileNames <- fread("/Users/nini/Desktop/2021lab/carolina/thickness_mmil_features.txt",data.table=F,header = F)FileNames$V2 <- gsub("UKB39k_Chen_GWAS_DM_310320_ChenT_bh_","",FileNames$V1)Sets <- gsub("_thickness_sumstat.fastGWA","",FileNames$V2)
for(i in 1:length(Sets)){ dat1 <- fread(paste0("/Users/nini/Desktop/2021lab/carolina/top/UKB39k_Chen_GWAS_DM_310320_",Sets[i],"_sumstat.fastGWA"),data.table=F)[,c("CHR","POS","P")] dat2 <- fread(paste0("/Users/nini/Desktop/2021lab/carolina/bottom/UKB39k_Chen_GWAS_DM_060420_",Sets[i],"_sumstat.fastGWA"),data.table=F)[,c("CHR","POS","P")] topcols <- c("grey72","grey42") botcols <- c("grey72","grey42") pcutoff <- 0.2 # cut away SNPs with P above this value, removing most SNPs, so it runs faster. ############### # Prep inputs # ############### colnames(dat1) <- c("chr","pos","p") -> colnames(dat2) dat1 <- dat1[complete.cases(dat1),] dat2 <- dat2[complete.cases(dat2),] ###### Create df with chr positions chrmaxpos <- data.frame("chr"=1:22,"maxpos"=NA,"genomestartpos"=NA) for(j in 1:22){ chrmaxpos$maxpos[j] <- max(c(dat1$pos[dat1$chr==j],dat2$pos[dat2$chr==j])) if(j==1){chrmaxpos$genomestartpos[j] <- 0 } else { chrmaxpos$genomestartpos[j] <- chrmaxpos$genomestartpos[j-1] + chrmaxpos$maxpos[j-1] } } ## label position chrmaxpos$labpos <- chrmaxpos$genomestartpos + 0.5*chrmaxpos$maxpos ####### Add genomic position to sumstats dat1$gpos <- NA -> dat2$gpos for(k in 1:22){ dat1$gpos[dat1$chr==k] <- dat1$pos[dat1$chr==k]+chrmaxpos$genomestartpos[k] dat2$gpos[dat2$chr==k] <- dat2$pos[dat2$chr==k]+chrmaxpos$genomestartpos[k] } ####### set graph parameters #maxp1 <- -log10(min(dat1$p)) #maxp2 <- -log10(min(dat2$p)) plotdat1 <- dat1[dat1$p<pcutoff,] plotdat2 <- dat2[dat2$p<pcutoff,] col1 <- rep(topcols,22)[plotdat1$chr] col2 <- rep(botcols,22)[plotdat2$chr] # if setting the y min as 20, if they pass 20 the y is set according to the max height of the indiviudal plot maxp1<- 20 maxp2<- 20 yAxisInterval <- 10 if (max(-log10(plotdat1$p))>20) { maxp1<- max(-log10(plotdat1$p))+0.5 yAxisInterval <- 20 } if ( max(-log10(plotdat2$p))>20) { maxp2<- max(-log10(plotdat2$p))+0.5 yAxisInterval <- 20 } if ( max(-log10(plotdat2$p))<25 | max(-log10(plotdat1$p))<25) { yAxisInterval <- 10 } axisLabNumTop <- ceiling(maxp1/yAxisInterval) # number of labels needed for each side of axis axisLabNumBottom <- ceiling(maxp2/yAxisInterval) axisLabAt <- c(seq(-yAxisInterval*axisLabNumBottom -4, -4,yAxisInterval),seq(4,yAxisInterval*(axisLabNumTop+1),yAxisInterval)) axisLabels <- c(seq(axisLabNumBottom*yAxisInterval,0,-yAxisInterval),0,seq(yAxisInterval,axisLabNumTop*yAxisInterval,yAxisInterval)) xlable <- c("1" , "", "3" ,"", "5" , "", "7" , "" , "9" , "" , "11", "", "13", "", "15", "","17", "" ,"19", "" ,"21" ,"")
Miami <- ggplot(plotdat1, aes(x=gpos, y=-log10(p)+4)) + theme_bw() + geom_hline(yintercept = -log10(5e-8)+4,color="navyblue",linetype="dashed",size=2) + geom_hline(yintercept = log10(5e-8)-4,color="navyblue",linetype="dashed",size=2) + geom_hline(yintercept = 4,color="black") + geom_hline(yintercept = -4,color="black") + geom_point(col=col1,size=3) + geom_point(data=plotdat2,aes(x=gpos,y=log10(p)-4),col=col2,inherit.aes = F, size=3) + scale_y_continuous(name="-log10(P-value) \n",limits=c(-maxp2-6, ifelse(maxp1<100,maxp1+6,110)),breaks=axisLabAt,labels = axisLabels) + geom_text(data=chrmaxpos,aes(x=labpos,y=0),label=as.character(1:22),size=4.5,inherit.aes = F) + expand_limits(y = 1) + # or some other arbitrarily large number #ggtitle(name1) + xlab(name2) + theme(plot.title=element_text(size=40,hjust = 0.5,margin = margin(b = -20),vjust = -6), axis.title.x=element_blank(), axis.text.x=element_blank(), axis.ticks.x=element_blank(), axis.title.y = element_text(size = 40,margin = margin(t = 0, r = -40, b = 0, l = 0)), axis.text.y = element_text(size = 40), panel.grid.minor = element_blank(), panel.grid.major = element_blank(), plot.background = element_blank(), #panel.border = element_blank(), plot.margin=unit(c(0.4,0,0.4,0.3),"cm"), #t,r,b,l panel.background = element_rect(colour = NA, fill = 'white')) ggsave(paste0(Path,"plots/normal/",Sets[i],"_THICKNESS_MainvsNoGlob.png"), plot = Miami, width = 15, height = 7,bg="transparent") }
Placed in power point and exported
For best quality image results when exporting from powerpoint:
Use print function in powerpoint to export into Postscripts.
Then open the Postscript file (.ps) and transform that into .tiff file. (.tiff files are large but high in quality, if you like smaller files .png is probably your second best option)
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