diff --git a/.gitignore b/.gitignore
index e75435c..b7a4307 100644
--- a/.gitignore
+++ b/.gitignore
@@ -47,3 +47,5 @@ po/*~
# RStudio Connect folder
rsconnect/
+
+/.quarto/
diff --git a/data/ChemDraw/Azido-PEG1-N-bis(PEG2-Tz).cdxml b/data/ChemDraw/Azido-PEG1-N-bis(PEG2-Tz).cdxml
new file mode 100644
index 0000000..41a2e60
--- /dev/null
+++ b/data/ChemDraw/Azido-PEG1-N-bis(PEG2-Tz).cdxml
@@ -0,0 +1,1017 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+NNNNONHOOONNNNONHOOONNN+N–
diff --git a/data/ChemDraw/Azido-PEG1-N-bis(PEG2-Tz).svg b/data/ChemDraw/Azido-PEG1-N-bis(PEG2-Tz).svg
new file mode 100644
index 0000000..47c055d
--- /dev/null
+++ b/data/ChemDraw/Azido-PEG1-N-bis(PEG2-Tz).svg
@@ -0,0 +1,139 @@
+
+
+
diff --git a/pdf/S02b.pdf b/pdf/S02b.pdf
new file mode 100644
index 0000000..f133c3f
Binary files /dev/null and b/pdf/S02b.pdf differ
diff --git a/supplementary_fig02.md b/supplementary_fig02.md
index eaccf9d..beb9b58 100644
--- a/supplementary_fig02.md
+++ b/supplementary_fig02.md
@@ -341,3 +341,77 @@ for(i in seq_along(mysamples)){
```
+
+Lets make this graph a little bit prettier, using
+[ColorBrewer2.org](https://colorbrewer2.org/) for color panels:
+
+``` r
+if(!require(RColorBrewer)){
+ install.packages('RColorBrewer')
+}
+```
+
+ Loading required package: RColorBrewer
+
+``` r
+library(RColorBrewer)
+
+mylabels <- c('AZdye594-PEG1-N-bis(PEG2-Tz)',
+ 'AZdye488-PEG1-N-bis(PEG2-Tz)',
+ 'AZdye594-DBCO',
+ 'AZdye488-DBCO',
+ 'Azido-PEG1-N-bis(PEG2-Tz)')
+
+color <- c(RColorBrewer::brewer.pal(6, 'PuOr')[c(5,1,6,2)], 'black')
+
+scale.factor.y <- 1.2 #adds some space between lines when we stack them on top.
+text.under.y <- 0.3 #placement of the text label under the trace.
+text.under.x <- 0.31 #placement of the text label under the trace.
+
+#normalize values
+normalize <- function(num_vec){
+ maxnv <- max(num_vec, na.rm = TRUE)
+ md<-num_vec[1]
+ return((num_vec-md) / (maxnv))
+}
+
+#create a new variable 'norm' which normalizes values for each compound
+trace$norm<-with(trace, ave(value, sample, FUN = normalize))
+
+quartz(width=5.5, height=5.6)
+par(mar=c(2,1,0,1))
+plot(trace$time[trace$sample == mysamples[1]],
+ trace$norm[trace$sample == mysamples[1]],
+ type='l',
+ xlab='',
+ ylab='',
+ ylim=c(-max(trace$norm)*text.under.y, scale.factor.y^2*max(trace$norm)*length(mysamples)),
+ xlim = c(1, 2.5),
+ axes=FALSE,
+ col=color[1]
+ )
+
+for(i in seq_along(mysamples)){
+ #k is a variable that adds some space for sample 3 and above so the two reactions are vertically seperated from the rest.
+ if(i > 2){
+ k <- 1.5
+ }else{
+ k <- 0
+ }
+ lines(trace$time[trace$sample == mysamples[i]],
+ trace$norm[trace$sample == mysamples[i]]+scale.factor.y*max(trace$norm)*(i-1)+k, col=color[i])
+
+ text(max(trace$time)*text.under.x, scale.factor.y*max(trace$norm)*(i-1)-max(trace$norm)*text.under.y+k, mylabels[i], col=color[i], pos=4, cex = 0.8)
+}
+```
+
+
+
+Lets save the figure as a PDF:
+
+``` r
+quartz.save(file='./pdf/S02b.pdf', type='pdf')
+```
+
+ quartz_off_screen
+ 2
diff --git a/supplementary_fig02.qmd b/supplementary_fig02.qmd
index 912eb64..84120e0 100644
--- a/supplementary_fig02.qmd
+++ b/supplementary_fig02.qmd
@@ -155,3 +155,69 @@ for(i in seq_along(mysamples)){
text(max(trace$time)*text.under.x, scale.factor.y*max(trace$value)*(i-1)-max(trace$value)*text.under.y+k, mysamples[i], col=i)
}
```
+
+Lets make this graph a little bit prettier, using [ColorBrewer2.org](https://colorbrewer2.org/) for color panels:
+
+```{r}
+if(!require(RColorBrewer)){
+ install.packages('RColorBrewer')
+}
+library(RColorBrewer)
+
+mylabels <- c('AZdye594-PEG1-N-bis(PEG2-Tz)',
+ 'AZdye488-PEG1-N-bis(PEG2-Tz)',
+ 'AZdye594-DBCO',
+ 'AZdye488-DBCO',
+ 'Azido-PEG1-N-bis(PEG2-Tz)')
+
+color <- c(RColorBrewer::brewer.pal(6, 'PuOr')[c(5,1,6,2)], 'black')
+
+scale.factor.y <- 1.2 #adds some space between lines when we stack them on top.
+text.under.y <- 0.3 #placement of the text label under the trace.
+text.under.x <- 0.31 #placement of the text label under the trace.
+
+#normalize values
+normalize <- function(num_vec){
+ maxnv <- max(num_vec, na.rm = TRUE)
+ md<-num_vec[1]
+ return((num_vec-md) / (maxnv))
+}
+
+#create a new variable 'norm' which normalizes values for each compound
+trace$norm<-with(trace, ave(value, sample, FUN = normalize))
+
+quartz(width=5.5, height=5.6)
+par(mar=c(2,1,0,1))
+plot(trace$time[trace$sample == mysamples[1]],
+ trace$norm[trace$sample == mysamples[1]],
+ type='l',
+ xlab='',
+ ylab='',
+ ylim=c(-max(trace$norm)*text.under.y, scale.factor.y^2*max(trace$norm)*length(mysamples)),
+ xlim = c(1, 2.5),
+ axes=FALSE,
+ col=color[1]
+ )
+
+for(i in seq_along(mysamples)){
+ #k is a variable that adds some space for sample 3 and above so the two reactions are vertically seperated from the rest.
+ if(i > 2){
+ k <- 1.5
+ }else{
+ k <- 0
+ }
+ lines(trace$time[trace$sample == mysamples[i]],
+ trace$norm[trace$sample == mysamples[i]]+scale.factor.y*max(trace$norm)*(i-1)+k, col=color[i])
+
+ text(max(trace$time)*text.under.x, scale.factor.y*max(trace$norm)*(i-1)-max(trace$norm)*text.under.y+k, mylabels[i], col=color[i], pos=4, cex = 0.8)
+}
+```
+
+Lets save the figure as a PDF:
+
+```{r}
+quartz.save(file='./pdf/S02b.pdf', type='pdf')
+```
+
+You can view the PDF here:
+
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