points(x,y, col=loc.colors)
text(x.txt,y,c("Drayton Harbor", "Big Beef Creek", "Lynch Cove", "North Bay", "Elliott Bay", "Sinclair Inlet", "Solo Point", "Hylebos Waterway"), cex=0.4)
leg.txt<-c("Low", "Moderate", "High", "Very High")
legend(-123.430741, 48.118146, legend=leg.txt, fill=c("blue3", "gold1", "orange2", "red3"), cex=0.25)
x.txt<-c(-122.3, -123.2, -123.2, -123.4, -122.0, -123.0, -122.3, -122.0)
map("state", "washington", fill=T, col="palegreen3")
points(x,y, col=loc.colors)
text(x.txt,y,c("Drayton Harbor", "Big Beef Creek", "Lynch Cove", "North Bay", "Elliott Bay", "Sinclair Inlet", "Solo Point", "Hylebos Waterway"), cex=0.4)
x.txt<-c(-122.2, -123.2, -123.2, -123.3, -122.1, -122.9, -122.4, -121.9)
map("state", "washington", fill=T, col="palegreen3")
points(x,y, col=loc.colors)
text(x.txt,y,c("Drayton Harbor", "Big Beef Creek", "Lynch Cove", "North Bay", "Elliott Bay", "Sinclair Inlet", "Solo Point", "Hylebos Waterway"), cex=0.4)
x.txt<-c(-122.4, -123.2, -123.2, -123.3, -122.1, -122.9, -122.4, -121.9)
map("state", "washington", fill=T, col="palegreen3")
.
points(x,y, col=loc.colors)
text(x.txt,y,c("Drayton Harbor", "Big Beef Creek", "Lynch Cove", "North Bay", "Elliott Bay", "Sinclair Inlet", "Solo Point", "Hylebos Waterway"), cex=0.4)
legend(-123.430741, 48.118146, legend=leg.txt, fill=c("blue3", "gold1", "orange2", "red3"), cex=0.25)
?map
map("state", "washington", fill=T, col="palegreen3", border="grey50", ylim=c(49.2, 47.0), xlim=c(-122.0,-124.0))
map("state", "washington", fill=T, col="palegreen3", border="grey50")
map("state", "washington", fill=T, col="palegreen3")
points(x,y, col=loc.colors)
text(x.txt,y,c("Drayton Harbor", "Big Beef Creek", "Lynch Cove", "North Bay", "Elliott Bay", "Sinclair Inlet", "Solo Point", "Hylebos Waterway"), cex=0.4, bold)
map("state", "washington", fill=T, col="palegreen3")
points(x,y, col=loc.colors, fill=T)
text(x.txt,y,c("Drayton Harbor", "Big Beef Creek", "Lynch Cove", "North Bay", "Elliott Bay", "Sinclair Inlet", "Solo Point", "Hylebos Waterway"), cex=0.4)
?map
map("state", "washington", fill=T, col="palegreen3", boundary=F)
y.txt<-c(48.7, 47.597041, 47.436205, 48.706982, 47.599821, 47.542182, 47.138708, 47.276488)
o
points(x,y, col=loc.colors)
text(x.txt,y.txt,c("Drayton Harbor", "Big Beef Creek", "Lynch Cove", "North Bay", "Elliott Bay", "Sinclair Inlet", "Solo Point", "Hylebos Waterway"), cex=0.4)
y.txt<-c(48.9, 47.597041, 47.436205, 48.706982, 47.599821, 47.542182, 47.138708, 47.276488)
map("state", "washington", fill=T, col="palegreen3", boundary=F)
points(x,y, col=loc.colors)
text(x.txt,y.txt,c("Drayton Harbor", "Big Beef Creek", "Lynch Cove", "North Bay", "Elliott Bay", "Sinclair Inlet", "Solo Point", "Hylebos Waterway"), cex=0.4)
legend(-123.430741, 48.118146, legend=leg.txt, fill=c("blue3", "gold1", "orange2", "red3"), cex=0.25)
library("maps")
library("mapdata")
library("mapproj")
library("Rgooglemaps")
library("Rgooglemap")
library("RgoogleMaps")
map("state", "washington", fill=T, col="palegreen3", boundary=F, fill=terrain.colors)
map("state", "washington", fill=T, boundary=F, fill=terrain.colors)
map("state", "washington", fill=terrain.colors, boundary=F)
map("state", "washington", fill="terrain.colors", boundary=F)
?map
map("state", "washington", fill=T,col=terrain.colors, boundary=F)
map("state", "washington", fill=T,col="terrain.colors", boundary=F)
library("GEOmaps")
library("GEOmap")
library("geomapdata")
library("RPMG")
library("akima")
library("splancs")
library("sp")
library("splancs")
?GEOmap
x<-c(-122.753796, -122.827754, -122.852089, -123.052859, -122.361794, -122.65349, -122.63235, -122.38929)
y<-c(48.976076, 47.597041, 47.436205, 48.706982, 47.599821, 47.542182, 47.138708, 47.276488)
BASICTOPOMAP(x,y,DOIMG=T, DOCONT=F)
?basictopomap
library("maps")
library("mapdata")
library("mapproj")
?map
map("county", regions=c("king", "whatcom"))
map("state", "washington", regions=c("whatcom", "king"))
map("county", "washington")
map("usa", "washington", fill=T, boundary=F, col="palegreen3")
map("state", "washington", fill=T, boundary=F, col="palegreen3")
map("state", "washington", fill=T, boundary=F, col="palegreen3", border=F)
map("state", "washington", fill=T, boundary=F, col="palegreen3", border=F, interior=F)
map("state", "washington", fill=T, boundary=F, col="palegreen3", border=F, interior=F, resolution=0)
map("state", "washington", fill=T, boundary=F, col="palegreen3", border=F, add=T, col="white")
text(-122.4, 48.9, expression(bold("Drayton Harbor")))
text(-122.4, 48.9, expression(bold("Drayton Harbor"), cex=0.5))
?text
map("state", "washington", fill=T, boundary=F, col="palegreen3", border=F, add=T, col="white")
map("state", "washington", fill=T, boundary=F, col="palegreen3", border=F)
text(-122.4, 48.9, expression(bold("Drayton Harbor")), cex=0.5)
map("state", "washington", fill=T, boundary=F, col="palegreen3", border=F)
text(-122.4, 48.9, expression(bold("Drayton Harbor")), cex=0.5, offset=1)
text(-122.4, 48.9, expression(bold("Drayton Harbor")), cex=0.5, offset=2)
map("state", "washington", fill=T, boundary=F, col="palegreen3", border=F)
text(-122.4, 48.9, expression(bold("Drayton Harbor")), cex=0.5, offset=2)
text(-123.2, 47.597041, expression(bold("Big Beef Creek")), cex=0.5)
text(-122.1, 47.599821, expression(bold("Elliot Bay")), cex=0.5)
text(-122.9, 47.542182, expression(bold("Sinclair Inlet")), cex=0.5)
text(-122.3, 47.138708, expression(bold("Solo Point")), cex=0.5)
text(-121.9, 47.276488, expression(bold("Hylebos Waterway")), cex=0.5)
points(x,y)
x1<-c(-122.753796, -122.827754, -122.361794, -122.65349, -122.63235, -122.38929)
y1<-c(48.976076, 47.597041, 47.599821, 47.542182, 47.138708, 47.276488)
points(x,y)
map("state", "washington", fill=T, boundary=F, col="palegreen3", border=F)
points(x1,y1)
points(x1,y1, cex=3)
?points
map("state", "washington", fill=T, boundary=F, col="palegreen3", border=F)
points(x1,y1, bg="black")
?points
points(x1,y1, pch=21:25, bg="black")
map("state", "washington", fill=T, boundary=F, col="palegreen3", border=F)
points(x1,y1, pch=21, bg="black")
text(-123.2, 47.597041, expression(bold("Big Beef Creek")), cex=0.5)#
text(-122.1, 47.599821, expression(bold("Elliot Bay")), cex=0.5)#
text(-122.9, 47.542182, expression(bold("Sinclair Inlet")), cex=0.5)#
text(-122.3, 47.138708, expression(bold("Solo Point")), cex=0.5)#
text(-121.9, 47.276488, expression(bold("Hylebos Waterway")), cex=0.5)
text(-122.4, 48.9, expression(bold("Drayton Harbor")), cex=0.5, offset=2)
map("state", "washington", fill=T, boundary=F, col="palegreen3", border=F)
points(x1,y1, pch=21, bg="firebrickred")
points(x1,y1, pch=21, bg="firebrickred3")
points(x1,y1, pch=21, bg="red")
text(-122.4, 48.9, expression(bold("Drayton Harbor")), cex=0.5, offset=2)#
text(-123.2, 47.597041, expression(bold("Big Beef Creek")), cex=0.5)#
text(-122.1, 47.599821, expression(bold("Elliot Bay")), cex=0.5)#
text(-122.9, 47.542182, expression(bold("Sinclair Inlet")), cex=0.5)#
text(-122.3, 47.138708, expression(bold("Solo Point")), cex=0.5)#
text(-121.9, 47.276488, expression(bold("Hylebos Waterway")), cex=0.5)
library("maps")
library("mapdata")
library("mapproj")
map("state", "washington", fill=T, col="palegreen3", boundary=F)
x<-c(-122.753796, -122.827754, -122.852089, -123.052859, -122.361794, -122.65349, -122.63235, -122.38929)
map("state", "washington", fill=T, boundary=F, col="palegreen3", border=F)
x1<-c(-122.753796, -122.827754, -122.361794, -122.65349, -122.63235, -122.38929)#
y1<-c(48.976076, 47.597041, 47.599821, 47.542182, 47.138708, 47.276488)
points(x1,y1, pch=21, bg="red")
text(-122.4, 48.9, expression(bold("Drayton Harbor")), cex=0.5, offset=2)#
text(-123.2, 47.597041, expression(bold("Big Beef Creek")), cex=0.5)#
text(-122.1, 47.599821, expression(bold("Elliot Bay")), cex=0.5)#
text(-122.9, 47.542182, expression(bold("Sinclair Inlet")), cex=0.5)#
text(-122.3, 47.138708, expression(bold("Solo Point")), cex=0.5)#
text(-121.9, 47.276488, expression(bold("Hylebos Waterway")), cex=0.5)
?merge
library(affy)
?edge
library(edgeR)
?edgeR
edgeR
edge
?edge
?seacarb
?pgas
library(seacarb)
?seacarb
?pgas
setwd("/Users/emmatimminsschiffman/Documents/Dissertation/Summer 2010")#
development<-read.csv("OADev1.csv", sep=",", header=T)#
raw.dev<-read.csv("OADev counts.csv", sep=",", header=T)
T1380<-development$Percent[1]#
T1840<-development$Percent[2]#
T2380<-development$Percent[3]#
T2840<-development$Percent[4]#
T3380<-development$Percent[5]#
T3840<-development$Percent[6]#
T4380<-development$Percent[7]#
T4840<-development$Percent[8]#
T5380<-development$Percent[9]#
T5840<-development$Percent[10]
error.bar<-function(x,y,upper, lower=upper, length=0.1)#
{if(length(x) !=length(y)|length(y) !=length(lower)|length(lower) !=length(upper))#
	stop("vectors must be same length")#
	arrows(x,y+upper, x, y-lower, angle=90, code=3, length=length)#
	}
cleav.mat<-matrix(data=c(T1380, T2380,T1840, T2840), ncol=2, nrow=2, byrow=T)
plot.cleav<-c(T1380, T2380,T1840, T2840)
bar.clv<-barplot(plot.cleav,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.names=1.2, cex.lab=1.5,ylim=c(0,.6))
plot.cleav<-c(T1380, T2380,T1840, T2840)
bar.clv<-barplot(plot.cleav,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.names=1.2, cex.lab=1.5,ylim=c(0,.6))
T1380<-development$Percent[1]
development<-read.csv("OADev1.csv", sep=",", header=T)
setwd("/Users/emmatimminsschiffman/Documents/Dissertation/Summer 2010")
getwd()
setwd("/Users/emmatimminsschiffman/Documents/Dissertation/Summer 2010")
getwd()
setwd("/Users/emmatimminsschiffman/Documents/Dissertation/Summer 2010")
development<-read.csv("OADev1.csv", sep=",", header=T)
raw.dev<-read.csv("OADev counts.csv", sep=",", header=T)
T1380<-development$Percent[1]#
T1840<-development$Percent[2]#
T2380<-development$Percent[3]#
T2840<-development$Percent[4]#
T3380<-development$Percent[5]#
T3840<-development$Percent[6]#
T4380<-development$Percent[7]#
T4840<-development$Percent[8]#
T5380<-development$Percent[9]#
T5840<-development$Percent[10]
error.bar<-function(x,y,upper, lower=upper, length=0.1)#
{if(length(x) !=length(y)|length(y) !=length(lower)|length(lower) !=length(upper))#
	stop("vectors must be same length")#
	arrows(x,y+upper, x, y-lower, angle=90, code=3, length=length)#
	}
cleav.mat<-matrix(data=c(T1380, T2380,T1840, T2840), ncol=2, nrow=2, byrow=T)
plot.cleav<-c(T1380, T2380,T1840, T2840)
bar.clv<-barplot(plot.cleav,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.names=1.2, cex.lab=1.5,ylim=c(0,.6))
T1380
T1840
T2380
bar.clv<-barplot(cleav.mat,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.names=1.2, cex.lab=1.5,ylim=c(0,.6))
bar.clv<-barplot(cleav.mat,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.names=1.15, cex.lab=1.5,ylim=c(0,.6))
bar.clv<-barplot(cleav.mat,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.names=1.1, cex.lab=1.5,ylim=c(0,.6))
bar.clv<-barplot(cleav.mat,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.names=1.05, cex.lab=1.5,ylim=c(0,.6))
bar.clv<-barplot(cleav.mat,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.lab=1.5,ylim=c(0,.6))
setwd("/Users/emmatimminsschiffman/Documents/Dissertation/Summer 2010")
raw.dev<-read.csv("OADev counts.csv", sep=",", header=T)
y.err.cleav<-c(sd(raw.dev$development[1:3]),sd(raw.dev$development[4:6]),sd(raw.dev$development[7:9]),sd(raw.dev$development[10:12]) )
error.bar(bar.clv,plot.cleav,y.err.cleav)
error.bar(bar.clv,cleav.mat,y.err.cleav)
bar.clv<-barplot(cleav.mat,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.lab=1.5,ylim=c(0,.6))
error.bar(bar.clv,cleav.mat,y.err.cleav)
bar.clv<-barplot(cleav.mat,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.lab=1.5,ylim=c(0,.62))
error.bar(bar.clv,cleav.mat,y.err.cleav)
bar.clv<-barplot(cleav.mat,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.lab=1.5,ylim=c(0,.65))
error.bar(bar.clv,cleav.mat,y.err.cleav)
hatch.dat<-c(T3380, T3840, T4380,T4840, T5380,T5840)
bar.hatch<-barplot(hatch.dat, beside=T,space=c(0.1,0.5), width=0.5, col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization (Hours)", ylab="Proportion Hatched", names.arg=c("5", "5", "17", "17", "24","24"), cex.names=1.5,cex.lab=1.5,ylim=c(0,1.1))
T3380
T3840
T4380
T4840
bar.hatch<-barplot(hatch.dat, beside=T,space=c(0,0,1,0,1,0,1), width=0.5, col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization (Hours)", ylab="Proportion Hatched", names.arg=c("5", "5", "17", "17", "24","24"), cex.names=1.5,cex.lab=1.5,ylim=c(0,1.1))
bar.hatch<-barplot(hatch.dat, beside=T,space=c(0,0,1,0,1,0), width=0.5, col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization (Hours)", ylab="Proportion Hatched", names.arg=c("5", "5", "17", "17", "24","24"), cex.names=1.5,cex.lab=1.5,ylim=c(0,1.1))
y.err.hatch<-c(sd(raw.dev$development[13:15]),sd(raw.dev$development[6:18]),sd(raw.dev$development[19:21]),sd(raw.dev$development[22:24]),sd(raw.dev$development[25:27]),sd(raw.dev$development[28:30]))
error.bar(bar.hatch,hatch.dat,y.err.hatch)
setwd("/Users/emmatimminsschiffman/Documents/Dissertation/Summer 2010")
development<-read.csv("OADev1.csv", sep=",", header=T)
T1380<-development$Percent[1]#
T1840<-development$Percent[2]#
T2380<-development$Percent[3]#
T2840<-development$Percent[4]#
T3380<-development$Percent[5]#
T3840<-development$Percent[6]#
T4380<-development$Percent[7]#
T4840<-development$Percent[8]#
T5380<-development$Percent[9]#
T5840<-development$Percent[10]
cleav.mat<-matrix(data=c(T1380, T2380,T1840, T2840), ncol=2, nrow=2, byrow=T)
bar.clv<-barplot(cleav.mat,beside=T, space=c(0,1),col=c("slateblue3", "steelblue3"), xlab="Time Post Fertilization", ylab="Proportion Cleavage", names.arg=c(rep("1 hr,2-cell",2), rep("2 hrs,>4-cell",2)), cex.lab=1.5,ylim=c(0,.65))
?setwd
library(seacarb)
c(1,2,3,4,5)
1:5
help(package='seacarb')
?seacarb
amp(s=35,T=25)
amp(S=35,T=25)
?alkalinity
alkalinity
data(alkalinity)
p2fCO2(T=16, 860)
p2fCO2(T=16, pCO2=860)
library(seacarb)
p2fCO2
f2pCO2
bjerrum
library(seacarb)
p2fCO2
f2pCO2
amp
buffer
carb
library(seacarb)
p2fCO2(T=25, pCO2=380)
p2fCO2
alkalinit
alkalinity
bjerrum
amp
p2fco2
p2fCO2
?aov
?TukeyHSD
?aov
?model.aov
?model
?ordi.monte
source("/Users/emmatimminsschiffman/Documents/Autumn 2010/Multivariate Stats/biostats.R")
ordi.monte
setwd('/Users/emmatimminsschiffman/Documents/Dissertation/proteomics')
oyster2.dat<-read.csv('oysters for pca spectral cutoff.csv', header=T, row.names=1)
oyster2.pca<-prcomp(oyster2.dat)
summary(oyster2.pca)
oyster2.plot<-ordiplot(oyster2.pca, choices=c(1,2), display='sites', xlab='PC 1 (16.7%)', ylab='PC 2 (14.0%)', type='n')
source("/Users/emmatimminsschiffman/Documents/Autumn 2010/Multivariate Stats/biostats.R")
oyster2.plot<-ordiplot(oyster2.pca, choices=c(1,2), display='sites', xlab='PC 1 (16.7%)', ylab='PC 2 (14.0%)', type='n')
library(vegan)
oyster2.plot<-ordiplot(oyster2.pca, choices=c(1,2), display='sites', xlab='PC 1 (16.7%)', ylab='PC 2 (14.0%)', type='n')
points(oyster2.plot, 'sites', pch=c(rep(1,4), rep(20,4)), col=c(rep('darkorchid4',8), rep('mediumblue', 8)), cex=2)
prot2.dat<-read.csv('expression average for pca spectral cutoff.csv', header=T, row.names=1)
prot2.pca<-prcomp(prot2.dat)
summary(prot2.pca)
prot2.plot<-ordiplot(prot2.pca, choices=c(1,2), display='sites', xlab='PC 1 (49.7%)', ylab='PC 2 (20.5%)', type='n')
points(highexp.plot, 'sites', pch=c(1,20), col=c(rep('darkorchid4',2), rep('mediumblue', 2)), cex=2)
points(prot2.plot, 'sites', pch=c(1,20), col=c(rep('darkorchid4',2), rep('mediumblue', 2)), cex=2)
prot2.plot<-ordiplot(prot2.pca, choices=c(1,2), display='sites', xlab='PC 1 (49.7%)', ylab='PC 2 (20.5%)', type='n')#
points(prot2.plot, 'sites', pch=c(1,20), col=c(rep('darkorchid4',2), rep('mediumblue', 2)), cex=2)
pca.eigenvec(prot2.pca, dim=3, digits=3, cutoff=0.1)