diff --git a/data/spectra/emission/01.txt b/data/spectra/emission/01.txt
new file mode 100755
index 0000000..5c1f3fd
--- /dev/null
+++ b/data/spectra/emission/01.txt
@@ -0,0 +1,219 @@
+365	14269.69728	365	560
+367	19388.74432	367	760
+369	15103.80667	369	590
+371	11728.70984	371	460
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+799	11697.39352	799	460
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\ No newline at end of file
diff --git a/data/spectra/emission/02.txt b/data/spectra/emission/02.txt
new file mode 100755
index 0000000..8f6d7de
--- /dev/null
+++ b/data/spectra/emission/02.txt
@@ -0,0 +1,219 @@
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+799	13198.63952	799	520
+801	14503.44775	801	570
\ No newline at end of file
diff --git a/data/spectra/emission/03.txt b/data/spectra/emission/03.txt
new file mode 100755
index 0000000..84e7dd9
--- /dev/null
+++ b/data/spectra/emission/03.txt
@@ -0,0 +1,88 @@
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+370	13800.50602	370	540
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+790	17873.10098	790	700
+795	13793.45577	795	540
+800	16108.82406	800	630
\ No newline at end of file
diff --git a/data/spectra/emission/04.txt b/data/spectra/emission/04.txt
new file mode 100755
index 0000000..12566f0
--- /dev/null
+++ b/data/spectra/emission/04.txt
@@ -0,0 +1,219 @@
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\ No newline at end of file
diff --git a/data/spectra/emission/05.txt b/data/spectra/emission/05.txt
new file mode 100755
index 0000000..f9cef89
--- /dev/null
+++ b/data/spectra/emission/05.txt
@@ -0,0 +1,219 @@
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\ No newline at end of file
diff --git a/data/spectra/emission/06.txt b/data/spectra/emission/06.txt
new file mode 100755
index 0000000..0c6dcb6
--- /dev/null
+++ b/data/spectra/emission/06.txt
@@ -0,0 +1,219 @@
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\ No newline at end of file
diff --git a/data/spectra/emission/07.txt b/data/spectra/emission/07.txt
new file mode 100755
index 0000000..50e9210
--- /dev/null
+++ b/data/spectra/emission/07.txt
@@ -0,0 +1,219 @@
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\ No newline at end of file
diff --git a/data/spectra/emission/08.txt b/data/spectra/emission/08.txt
new file mode 100755
index 0000000..4a078d3
--- /dev/null
+++ b/data/spectra/emission/08.txt
@@ -0,0 +1,219 @@
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\ No newline at end of file
diff --git a/data/spectra/emission/09.txt b/data/spectra/emission/09.txt
new file mode 100755
index 0000000..f2c8ffc
--- /dev/null
+++ b/data/spectra/emission/09.txt
@@ -0,0 +1,219 @@
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\ No newline at end of file
diff --git a/data/spectra/emission/10.txt b/data/spectra/emission/10.txt
new file mode 100755
index 0000000..038ac0d
--- /dev/null
+++ b/data/spectra/emission/10.txt
@@ -0,0 +1,219 @@
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\ No newline at end of file
diff --git a/data/spectra/emission/11.txt b/data/spectra/emission/11.txt
new file mode 100755
index 0000000..752c28c
--- /dev/null
+++ b/data/spectra/emission/11.txt
@@ -0,0 +1,219 @@
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\ No newline at end of file
diff --git a/data/spectra/emission/12.txt b/data/spectra/emission/12.txt
new file mode 100755
index 0000000..f27ecbc
--- /dev/null
+++ b/data/spectra/emission/12.txt
@@ -0,0 +1,219 @@
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\ No newline at end of file
diff --git a/data/spectra/emission/13.txt b/data/spectra/emission/13.txt
new file mode 100755
index 0000000..56f28aa
--- /dev/null
+++ b/data/spectra/emission/13.txt
@@ -0,0 +1,219 @@
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\ No newline at end of file
diff --git a/data/spectra/emission/14.txt b/data/spectra/emission/14.txt
new file mode 100755
index 0000000..bb32494
--- /dev/null
+++ b/data/spectra/emission/14.txt
@@ -0,0 +1,219 @@
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\ No newline at end of file
diff --git a/data/spectra/emission/15.txt b/data/spectra/emission/15.txt
new file mode 100755
index 0000000..7aaad57
--- /dev/null
+++ b/data/spectra/emission/15.txt
@@ -0,0 +1,219 @@
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\ No newline at end of file
diff --git a/data/spectra/emission/16.txt b/data/spectra/emission/16.txt
new file mode 100755
index 0000000..3147dd5
--- /dev/null
+++ b/data/spectra/emission/16.txt
@@ -0,0 +1,219 @@
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+379	40992.29628	379	580
+381	37562.01276	381	530
+383	40345.41336	383	570
+385	43862.75203	385	620
+387	57337.01423	387	810
+389	46649.70314	389	660
+391	31064.671	391	440
+393	34744.38063	393	490
+395	40934.43433	395	580
+397	43875.16807	397	620
+399	39534.06283	399	560
+401	47306.36165	401	670
+403	35473.57219	403	500
+405	50290.40941	405	710
+407	33987.11322	407	480
+409	36829.80381	409	520
+411	29816.83942	411	420
+413	36814.15929	413	520
+415	45412.61619	415	640
+417	45985.14326	417	650
+419	41114.3404	419	580
+421	40240.02824	421	570
+423	44560.75824	423	630
+425	30431.70559	425	430
+427	41725.60113	427	590
+429	44513.5307	429	630
+431	40402.60845	431	570
+433	45296.90707	433	640
+435	44557.60662	435	630
+437	34614.29782	437	490
+439	36055.14316	439	510
+441	43201.13314	441	610
+443	44636.5311	443	630
+445	41064.85415	445	580
+447	45325.77904	447	640
+449	54340.15526	449	770
+451	36767.30538	451	520
+453	41672.55262	453	590
+455	43912.45839	455	620
+457	34719.76192	457	490
+459	41050.32203	459	580
+461	45322.56922	461	640
+463	47383.30976	463	670
+465	41752.17607	465	590
+467	45920.16955	467	650
+469	41823.20834	469	590
+471	36116.42235	471	510
+473	43934.24036	473	620
+475	38976.68486	475	550
+477	43167.50407	477	610
+479	36866.35945	479	520
+481	38817.136	481	550
+483	27628.22329	483	390
+485	41740.36081	485	590
+487	45264.87022	487	640
+489	33929.45501	489	480
+491	43841.04087	491	620
+493	36136.89506	493	510
+495	41758.08621	495	590
+497	31165.88752	497	440
+499	41749.22162	499	590
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+515	36811.55316	515	520
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+547	46079.6824	547	650
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+579	221451.81831	579	3130
+581	259896.60789	581	3670
+583	350852.37321	583	4960
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+587	532946.42225	587	7530
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+593	1.02613E6	593	14490
+595	1.29206E6	595	18240
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+613	2.95099E6	613	41730
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+629	2.02857E6	629	28690
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+639	1.33756E6	639	19000
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+643	1.10221E6	643	15680
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+697	236181.61309	697	3350
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+707	155995.17833	707	2200
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+715	133022.00524	715	1880
+717	127199.4912	717	1800
+719	96922.53272	719	1370
+721	96140.25166	721	1360
+723	103930.99548	723	1470
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+731	90287.08471	731	1280
+733	77004.59202	733	1090
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+739	86445.12152	739	1220
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+743	72227.72978	743	1020
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+749	71413.42007	749	1010
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+797	41006.78733	797	580
+799	49389.68461	799	700
+801	42348.95539	801	600
\ No newline at end of file
diff --git a/data/spectra/emission/17.txt b/data/spectra/emission/17.txt
new file mode 100755
index 0000000..fb5ab45
--- /dev/null
+++ b/data/spectra/emission/17.txt
@@ -0,0 +1,219 @@
+365	37474.36895	365	530
+367	40325.43332	367	570
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+629	2.08664E6	629	29480
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+721	115553.66511	721	1630
+723	92041.91447	723	1300
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+731	78578.50772	731	1110
+733	59528.02778	733	840
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+739	78517.36578	739	1110
+741	72284.03373	741	1020
+743	72740.11299	743	1030
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+749	70108.34927	749	990
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+769	57332.95583	769	810
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+777	49627.79156	777	700
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+787	33967.87205	787	480
+789	41802.46564	789	590
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+797	48254.3287	797	680
+799	32600.9922	799	460
+801	29806.25931	801	420
\ No newline at end of file
diff --git a/figure01.qmd b/figure01.qmd
new file mode 100644
index 0000000..218ab90
--- /dev/null
+++ b/figure01.qmd
@@ -0,0 +1,116 @@
+---
+title: "figure01"
+format: html
+---
+
+## Emission plot
+
+```{r}
+files<-dir('data/spectra/emission', full.names = TRUE)
+
+spectra<-read.table(files[1], sep='\t')
+spectra$sample <- 1
+
+for(i in seq_along(files)[-1]){
+  spectra.tmp <-read.table(files[i], sep='\t')
+  spectra.tmp$sample <- i
+  spectra <- rbind(spectra, spectra.tmp)
+}
+
+spectra$fluor <- NA
+
+spectra$fluor[spectra$sample %in% seq(9,17)] <- 594
+spectra$fluor[!(spectra$sample %in% seq(9,17))] <- 488
+
+spectra$status <- NA
+
+status<-c('fluor', 'quench', 'fluor',
+          'quench', 'quench', 'unquench',
+          'unquench', 'unquench', 'unquench',
+          'fluor', 'fluor', 'fluor',
+          'quench', 'quench', 'quench',
+          'unquench', 'unquench', 'unquench')
+k<-1
+for(i in unique(spectra$sample)){
+  
+  
+  spectra$status[spectra$sample==i]<-status[i]
+
+}
+
+
+library(dplyr)
+spec<- spectra %>% 
+  group_by(fluor, status, V3) %>% 
+  summarise(emission=mean(V4))
+
+spec$emission[spec$fluor == 488]<-spec$emission[spec$fluor == 488]/max(spec$emission[spec$fluor == 488 & spec$status == 'fluor'])
+spec$emission[spec$fluor == 594]<-spec$emission[spec$fluor == 594]/max(spec$emission[spec$fluor == 594 & spec$status == 'fluor'])
+
+spec$emission <- spec$emission - mean(spec$emission[1:50])
+
+
+col2hex <- function(cname)
+{
+  colMat <- col2rgb(cname)
+  rgb(
+    red=colMat[1,]/255,
+    green=colMat[2,]/255,
+    blue=colMat[3,]/255
+  )
+}
+
+spec<- spec[-which(spec$status == 'unquench'),]
+
+quartz(width = 130.1729/20, height = 83.8626/20)
+par(yaxs='i', xaxs='i', mar=c(4,4,1,1))
+plot(0,0, type='n', xlim=c(450,750), ylim=c(0,1), ylab='Emission', xlab="Wavelength (nm)", las=1, axes=F)
+axis(2, las=1, at=c(0,0.5,1))
+
+color <- c('green3', 'green4', 'red', 'red4')
+unique_samples <- unique( paste(spec$fluor, spec$status) )
+names(spec)<-c("fluor" ,   "status" ,  "wavelength"     ,  "emission")
+
+peak.max <- numeric()
+# Loop through each unique sample and create a polygon plot
+for (sample_name in unique_samples) {
+  # Subset the data for the current sample
+  sample_data <- spec[paste(spec$fluor, spec$status) == sample_name, ]
+  
+  # Create a polygon plot for the current sample
+  polygon(c(sample_data$wavelength, 
+            sample_data$wavelength[nrow(sample_data)], 
+            sample_data$wavelength[1],
+            sample_data$wavelength[1]), 
+          
+          c(sample_data$emission, 0, 0, sample_data$emission[1]), 
+          col = paste0( col2hex( color[match(sample_name, unique_samples)] ), '70' ),
+          border = color[match(sample_name, unique_samples)], lwd=2, xpd=F )
+  
+  # Add a legend for sample names
+  legend("topright", legend = unique_samples, fill = color)
+  
+  peak.max <- c(peak.max, sample_data$wavelength[which.max(sample_data$emission)] )
+}
+
+axis(1, at=seq(300,800,by=50))
+
+```
+
+Save the plot.
+
+```{r}
+quartz.save(file="pdf/figure01_c.pdf", type='pdf')
+```
+
+Then compute quench ratio:
+```{r}
+quench.ratio <- spec %>% group_by(fluor, status) %>% summarise(max(emission))
+
+AZdye488<-quench.ratio$`max(emission)`[1]/quench.ratio$`max(emission)`[2]
+
+AZdye594<-quench.ratio$`max(emission)`[3]/quench.ratio$`max(emission)`[4]
+
+round(AZdye488, 2)
+round(AZdye594, 2)
+```
diff --git a/pdf/S02b.pdf b/pdf/S02b.pdf
index c8bf0fa..69e63c6 100644
Binary files a/pdf/S02b.pdf and b/pdf/S02b.pdf differ
diff --git a/pdf/S02b_excitation.pdf b/pdf/S02b_excitation.pdf
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