added figure01 qmd

figure01.md

@@ -0,0 +1,151 @@
+# figure01
+
+- [Emission plot](#emission-plot)
+
+## 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$sample==i]<-status[i]
+
+}
+
+
+library(dplyr)
+```
+
+
+    Attaching package: 'dplyr'
+
+    The following objects are masked from 'package:stats':
+
+        filter, lag
+
+    The following objects are masked from 'package:base':
+
+        intersect, setdiff, setequal, union
+
+``` r
+spec<- spectra %>% 
+  group_by(fluor, status, V3) %>% 
+  summarise(emission=mean(V4))
+```
+
+    `summarise()` has grouped output by 'fluor', 'status'. You can override using
+    the `.groups` argument.
+
+``` r
+spec$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$emission)] )
+}
+
+axis(1, at=seq(300,800,by=50))
+```
+
+![](figure01_files/figure-commonmark/unnamed-chunk-1-1.png)
+
+Save the plot.
+
+``` r
+quartz.save(file="pdf/figure01_c.pdf", type='pdf')
+```
+
+    quartz_off_screen 
+                    2 
+
+Then compute quench ratio:
+
+``` r
+quench.ratio <- spec %>% group_by(fluor, status) %>% summarise(max(emission))
+```
+
+    `summarise()` has grouped output by 'fluor'. You can override using the
+    `.groups` argument.
+
+``` r
+AZdye488<-quench.ratio$`max(emission)`[1]/quench.ratio$`max(emission)`[2]
+
+AZdye594<-quench.ratio$`max(emission)`[3]/quench.ratio$`max(emission)`[4]
+
+round(AZdye488, 2)
+```
+
+    [1] 5.74
+
+``` r
+round(AZdye594, 2)
+```
+
+    [1] 2.88

figure01.qmd

@@ -1,6 +1,7 @@
 ---
 title: "figure01"
-format: html
+format: gfm
+toc: true
 ---
 
 ## Emission plot