-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy path.Rhistory
132 lines (132 loc) · 11.1 KB
/
.Rhistory
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
library(plotly)
.libPaths()
library(devtools)
instal.github("seaflow-uw/popcycle")
install.github("seaflow-uw/popcycle")
install_github("seaflow-uw/popcycle")
install.packages("devtools")
install.packages("BiocManager", repos='http://cran.us.r-project.org')
BiocManager::install("flowDensity", update=F)
install.packages("rgeos")
BiocManager::install("flowDensity", update=F)
BiocManager::install("flowDensity", update=F)
BiocManager::install("flowDensity", update=F)
install.packages("rgeos")
# Load packages
library(viridis)
library(tidyverse)
# Load custom functions
# To install FCSplankton library the first time, follow these two steps
# library(devtools)
# install_github("fribalet/FCSplankton")
library(FCSplankton)
.libPaths()
library(scales)
library(scales)
library(viridis)
path.to.git.repository <- "~/Documents/DATA/Codes/fsc-poc-calibration"
setwd(path.to.git.repository)
mie <- read.csv("calibrated-mie.csv")
inst <- 740
merge <- read.csv(paste0(inst,"-Qc-cultures.csv"))
merge2 <- subset(merge, Sample.ID !="Phaeodactylum tricornutum") # remove non-spherical cells
merge2 <- merge2[order(merge2$norm.fsc),]
plot(merge2$norm.fsc,merge2$pgC.cell, log='xy', yaxt='n', xaxt='n', pch=NA,xlim=c(0.002,10), ylim=c(0.005,100), ylab=expression(paste("Qc (pgC cell"^{-1},")")), xlab="Normalized scatter (dimensionless)", main=paste(inst))
with(merge2, arrows(norm.fsc, pgC.cell - pgC.cell.sd, norm.fsc, pgC.cell + pgC.cell.sd, code = 3, length=0, col='grey', lwd=2))
with(merge2, arrows(norm.fsc-norm.fsc.sd, pgC.cell, norm.fsc+norm.fsc.sd, pgC.cell, code = 3, length=0,col='grey',lwd=2))
points(merge2$norm.fsc,merge2$pgC.cell,bg=alpha(viridis(nrow(merge2)),0.5),cex=2, pch=21)
axis(2, at=c(0.005,0.01,0.02,0.05,0.1,0.2,0.5,1,2,5,10,20,50,100,1000), labels=c(0.005,0.01, 0.02,0.05,0.1,0.2,0.5,1,2,5,10,20,50,100,1000), las=1)
axis(1, at=c(0.002,0.005,0.01,0.02,0.05,0.1,0.2,0.5,1,2,5,10),labels=c(0.002,0.005,0.01,0.02,0.05,0.1,0.2,0.5,1,2,5,10))
legend("topleft",legend=c(as.vector(merge2$Sample.ID),"Mie-based model (n = 1.38 +/- 0.3)"), cex=0.5,pch=c(rep(21,nrow(merge2)),NA), lwd=c(rep(NA,nrow(merge2)),2), bty='n',
pt.bg=alpha(viridis(nrow(merge2)),0.5), col=c(rep(1,nrow(merge2)),'red3'), text.font=c(rep(3,nrow(merge2)),1))
plot(merge2$norm.fsc,merge2$pgC.cell, log='xy', yaxt='n', xaxt='n', pch=NA,xlim=c(0.002,10), ylim=c(0.005,100), ylab=expression(paste("Qc (pgC cell"^{-1},")")), xlab="Normalized scatter (dimensionless)", main=paste(inst))
with(merge2, arrows(norm.fsc, pgC.cell - pgC.cell.sd, norm.fsc, pgC.cell + pgC.cell.sd, code = 3, length=0, col='grey', lwd=2))
with(merge2, arrows(norm.fsc-norm.fsc.sd, pgC.cell, norm.fsc+norm.fsc.sd, pgC.cell, code = 3, length=0,col='grey',lwd=2))
points(merge2$norm.fsc,merge2$pgC.cell,bg=alpha(viridis(nrow(merge2)),0.5),cex=2, pch=21)
axis(2, at=c(0.005,0.01,0.02,0.05,0.1,0.2,0.5,1,2,5,10,20,50,100,1000), labels=c(0.005,0.01, 0.02,0.05,0.1,0.2,0.5,1,2,5,10,20,50,100,1000), las=1)
axis(1, at=c(0.002,0.005,0.01,0.02,0.05,0.1,0.2,0.5,1,2,5,10),labels=c(0.002,0.005,0.01,0.02,0.05,0.1,0.2,0.5,1,2,5,10))
legend("topleft",legend=c(as.vector(merge2$Sample.ID)), cex=0.5,pch=c(rep(21,nrow(merge2))), bty='n',
pt.bg=alpha(viridis(nrow(merge2)),0.5), col=c(rep(1,nrow(merge2))), text.font=c(rep(3,nrow(merge2)),1))
abline(1,1)
abline(log10(2.25), 1.14)
abline(log10(3.25), 1.14)
lm(norm.fsc, pgC.cell, data=merge2)
lm(norm.fsc ~ pgC.cell, data=merge2)
plot(lm(norm.fsc ~ pgC.cell, data=merge2))
lm(norm.fsc ~ pgC.cell, data=merge2)
plot(merge2$norm.fsc,merge2$pgC.cell, log='xy', yaxt='n', xaxt='n', pch=NA,xlim=c(0.002,10), ylim=c(0.005,100), ylab=expression(paste("Qc (pgC cell"^{-1},")")), xlab="Normalized scatter (dimensionless)", main=paste(inst))
with(merge2, arrows(norm.fsc, pgC.cell - pgC.cell.sd, norm.fsc, pgC.cell + pgC.cell.sd, code = 3, length=0, col='grey', lwd=2))
with(merge2, arrows(norm.fsc-norm.fsc.sd, pgC.cell, norm.fsc+norm.fsc.sd, pgC.cell, code = 3, length=0,col='grey',lwd=2))
points(merge2$norm.fsc,merge2$pgC.cell,bg=alpha(viridis(nrow(merge2)),0.5),cex=2, pch=21)
axis(2, at=c(0.005,0.01,0.02,0.05,0.1,0.2,0.5,1,2,5,10,20,50,100,1000), labels=c(0.005,0.01, 0.02,0.05,0.1,0.2,0.5,1,2,5,10,20,50,100,1000), las=1)
axis(1, at=c(0.002,0.005,0.01,0.02,0.05,0.1,0.2,0.5,1,2,5,10),labels=c(0.002,0.005,0.01,0.02,0.05,0.1,0.2,0.5,1,2,5,10))
legend("topleft",legend=c(as.vector(merge2$Sample.ID)), cex=0.5,pch=c(rep(21,nrow(merge2))), bty='n',
pt.bg=alpha(viridis(nrow(merge2)),0.5), col=c(rep(1,nrow(merge2))), text.font=c(rep(3,nrow(merge2)),1))
abline(0.06201, 0.24570)
abline( 0.24570, 0.06201)
lm(pgC.cell ~ norm.fsc, data=merge2)
abline(-0.2213, 4.0437)
lm(pgC.cell ~ norm.fsc, data=log10(merge2))
lm(pgC.cell ~ norm.fsc, data=log10(merge2[,c("pgC.cell","norm.fsc")]))
abline(0.5239, 1.0462)
abline(0.5239, 1.0462, lwd=2, col='red3')
plot(merge2$norm.fsc,merge2$pgC.cell, log='xy', yaxt='n', xaxt='n', pch=NA,xlim=c(0.002,10), ylim=c(0.005,100), ylab=expression(paste("Qc (pgC cell"^{-1},")")), xlab="Normalized scatter (dimensionless)", main=paste(inst))
with(merge2, arrows(norm.fsc, pgC.cell - pgC.cell.sd, norm.fsc, pgC.cell + pgC.cell.sd, code = 3, length=0, col='grey', lwd=2))
with(merge2, arrows(norm.fsc-norm.fsc.sd, pgC.cell, norm.fsc+norm.fsc.sd, pgC.cell, code = 3, length=0,col='grey',lwd=2))
points(merge2$norm.fsc,merge2$pgC.cell,bg=alpha(viridis(nrow(merge2)),0.5),cex=2, pch=21)
axis(2, at=c(0.005,0.01,0.02,0.05,0.1,0.2,0.5,1,2,5,10,20,50,100,1000), labels=c(0.005,0.01, 0.02,0.05,0.1,0.2,0.5,1,2,5,10,20,50,100,1000), las=1)
axis(1, at=c(0.002,0.005,0.01,0.02,0.05,0.1,0.2,0.5,1,2,5,10),labels=c(0.002,0.005,0.01,0.02,0.05,0.1,0.2,0.5,1,2,5,10))
legend("topleft",legend=c(as.vector(merge2$Sample.ID)), cex=0.5,pch=c(rep(21,nrow(merge2))), bty='n',
pt.bg=alpha(viridis(nrow(merge2)),0.5), col=c(rep(1,nrow(merge2))), text.font=c(rep(3,nrow(merge2)),1))
abline(0.5239, 1.0462, lwd=2, col='red3')
pdf("Qc-scatter.pdf",width=6, height=6)
plot(merge2$norm.fsc,merge2$pgC.cell, log='xy', yaxt='n', xaxt='n', pch=NA,xlim=c(0.002,10), ylim=c(0.005,100), ylab=expression(paste("Qc (pgC cell"^{-1},")")), xlab="Normalized scatter (dimensionless)")
with(merge2, arrows(norm.fsc, pgC.cell - pgC.cell.sd, norm.fsc, pgC.cell + pgC.cell.sd, code = 3, length=0, col='grey', lwd=2))
with(merge2, arrows(norm.fsc-norm.fsc.sd, pgC.cell, norm.fsc+norm.fsc.sd, pgC.cell, code = 3, length=0,col='grey',lwd=2))
points(merge2$norm.fsc,merge2$pgC.cell,bg=alpha(viridis(nrow(merge2)),0.5),cex=2, pch=21)
axis(2, at=c(0.005,0.01,0.02,0.05,0.1,0.2,0.5,1,2,5,10,20,50,100,1000), labels=c(0.005,0.01, 0.02,0.05,0.1,0.2,0.5,1,2,5,10,20,50,100,1000), las=1)
axis(1, at=c(0.002,0.005,0.01,0.02,0.05,0.1,0.2,0.5,1,2,5,10),labels=c(0.002,0.005,0.01,0.02,0.05,0.1,0.2,0.5,1,2,5,10))
legend("topleft",legend=c(as.vector(merge2$Sample.ID)), cex=0.5,pch=c(rep(21,nrow(merge2))), bty='n',
pt.bg=alpha(viridis(nrow(merge2)),0.5), col=c(rep(1,nrow(merge2))), text.font=c(rep(3,nrow(merge2)),1))
abline(0.5239, 1.0462, lwd=2, col='red3')
dev.off()
plot(merge2$norm.fsc,merge2$pgC.cell, log='xy', yaxt='n', xaxt='n', pch=NA,xlim=c(0.002,10), ylim=c(0.005,100), ylab=expression(paste("Qc (pgC cell"^{-1},")")), xlab="Normalized scatter (dimensionless)")
with(merge2, arrows(norm.fsc, pgC.cell - pgC.cell.sd, norm.fsc, pgC.cell + pgC.cell.sd, code = 3, length=0, col='grey', lwd=2))
with(merge2, arrows(norm.fsc-norm.fsc.sd, pgC.cell, norm.fsc+norm.fsc.sd, pgC.cell, code = 3, length=0,col='grey',lwd=2))
points(merge2$norm.fsc,merge2$pgC.cell,bg=alpha(viridis(nrow(merge2)),0.5),cex=2, pch=21)
axis(2, at=c(0.005,0.01,0.02,0.05,0.1,0.2,0.5,1,2,5,10,20,50,100,1000), labels=c(0.005,0.01, 0.02,0.05,0.1,0.2,0.5,1,2,5,10,20,50,100,1000), las=1)
axis(1, at=c(0.002,0.005,0.01,0.02,0.05,0.1,0.2,0.5,1,2,5,10),labels=c(0.002,0.005,0.01,0.02,0.05,0.1,0.2,0.5,1,2,5,10))
legend("topleft",legend=c(as.vector(merge2$Sample.ID)), cex=0.5,pch=c(rep(21,nrow(merge2))), bty='n',
pt.bg=alpha(viridis(nrow(merge2)),0.5), col=c(rep(1,nrow(merge2))), text.font=c(rep(3,nrow(merge2)),1))
abline(0.5239, 1.0462, lwd=2, col='red3')
plot(merge2$norm.fsc,merge2$pgC.cell, log='xy', yaxt='n', xaxt='n', pch=NA,xlim=c(0.002,10), ylim=c(0.005,100), ylab=expression(paste("Qc (pgC cell"^{-1},")")), xlab="Normalized scatter (dimensionless)")
with(merge2, arrows(norm.fsc, pgC.cell - pgC.cell.sd, norm.fsc, pgC.cell + pgC.cell.sd, code = 3, length=0, col='grey', lwd=2))
with(merge2, arrows(norm.fsc-norm.fsc.sd, pgC.cell, norm.fsc+norm.fsc.sd, pgC.cell, code = 3, length=0,col='grey',lwd=2))
points(merge2$norm.fsc,merge2$pgC.cell,bg=alpha(viridis(nrow(merge2)),0.5),cex=2, pch=21)
axis(2, at=c(0.005,0.01,0.02,0.05,0.1,0.2,0.5,1,2,5,10,20,50,100,1000), labels=c(0.005,0.01, 0.02,0.05,0.1,0.2,0.5,1,2,5,10,20,50,100,1000), las=1)
axis(1, at=c(0.002,0.005,0.01,0.02,0.05,0.1,0.2,0.5,1,2,5,10),labels=c(0.002,0.005,0.01,0.02,0.05,0.1,0.2,0.5,1,2,5,10))
legend("topleft",legend=c(as.vector(merge2$Sample.ID)), cex=0.5,pch=c(rep(21,nrow(merge2))), bty='n',
pt.bg=alpha(viridis(nrow(merge2)),0.5), col=c(rep(1,nrow(merge2))), text.font=c(rep(3,nrow(merge2)),1))
abline(0.5239, 1.0462, lwd=2, col='red3')
pdf("~/home/Desktop/Qc-scatter.pdf",width=6, height=6)
plot(merge2$norm.fsc,merge2$pgC.cell, log='xy', yaxt='n', xaxt='n', pch=NA,xlim=c(0.002,10), ylim=c(0.005,100), ylab=expression(paste("Qc (pgC cell"^{-1},")")), xlab="Normalized scatter (dimensionless)")
with(merge2, arrows(norm.fsc, pgC.cell - pgC.cell.sd, norm.fsc, pgC.cell + pgC.cell.sd, code = 3, length=0, col='grey', lwd=2))
with(merge2, arrows(norm.fsc-norm.fsc.sd, pgC.cell, norm.fsc+norm.fsc.sd, pgC.cell, code = 3, length=0,col='grey',lwd=2))
points(merge2$norm.fsc,merge2$pgC.cell,bg=alpha(viridis(nrow(merge2)),0.5),cex=2, pch=21)
axis(2, at=c(0.005,0.01,0.02,0.05,0.1,0.2,0.5,1,2,5,10,20,50,100,1000), labels=c(0.005,0.01, 0.02,0.05,0.1,0.2,0.5,1,2,5,10,20,50,100,1000), las=1)
axis(1, at=c(0.002,0.005,0.01,0.02,0.05,0.1,0.2,0.5,1,2,5,10),labels=c(0.002,0.005,0.01,0.02,0.05,0.1,0.2,0.5,1,2,5,10))
legend("topleft",legend=c(as.vector(merge2$Sample.ID)), cex=0.5,pch=c(rep(21,nrow(merge2))), bty='n',
pt.bg=alpha(viridis(nrow(merge2)),0.5), col=c(rep(1,nrow(merge2))), text.font=c(rep(3,nrow(merge2)),1))
abline(0.5239, 1.0462, lwd=2, col='red3')
dev.off()
pdf("~/Desktop/Qc-scatter.pdf",width=6, height=6)
plot(merge2$norm.fsc,merge2$pgC.cell, log='xy', yaxt='n', xaxt='n', pch=NA,xlim=c(0.002,10), ylim=c(0.005,100), ylab=expression(paste("Qc (pgC cell"^{-1},")")), xlab="Normalized scatter (dimensionless)")
with(merge2, arrows(norm.fsc, pgC.cell - pgC.cell.sd, norm.fsc, pgC.cell + pgC.cell.sd, code = 3, length=0, col='grey', lwd=2))
with(merge2, arrows(norm.fsc-norm.fsc.sd, pgC.cell, norm.fsc+norm.fsc.sd, pgC.cell, code = 3, length=0,col='grey',lwd=2))
points(merge2$norm.fsc,merge2$pgC.cell,bg=alpha(viridis(nrow(merge2)),0.5),cex=2, pch=21)
axis(2, at=c(0.005,0.01,0.02,0.05,0.1,0.2,0.5,1,2,5,10,20,50,100,1000), labels=c(0.005,0.01, 0.02,0.05,0.1,0.2,0.5,1,2,5,10,20,50,100,1000), las=1)
axis(1, at=c(0.002,0.005,0.01,0.02,0.05,0.1,0.2,0.5,1,2,5,10),labels=c(0.002,0.005,0.01,0.02,0.05,0.1,0.2,0.5,1,2,5,10))
legend("topleft",legend=c(as.vector(merge2$Sample.ID)), cex=0.5,pch=c(rep(21,nrow(merge2))), bty='n',
pt.bg=alpha(viridis(nrow(merge2)),0.5), col=c(rep(1,nrow(merge2))), text.font=c(rep(3,nrow(merge2)),1))
abline(0.5239, 1.0462, lwd=2, col='red3')
dev.off()