--- a/README.markdown Sun Feb 09 13:23:50 2020 -0500
+++ b/README.markdown Sun Feb 09 18:06:22 2020 -0500
@@ -614,3 +614,41 @@
idea behind it (computing a dependency graph and using it to rebuild things) is
sound, but the implementation is a clusterfuck of string processing and horrific
syntax. It really gives me the urge to create Yet Another Build System. Sigh.
+
+Eventually `cuffdiff` finished. Time to move on. Tried to install cummerbund
+in R, but ran into a bunch of errors. Had to install numerous third-party
+dependencies outside of R:
+
+* `libcurl4-openssl-dev`
+* `libxml2-dev`
+* `libmariadbclient-dev`
+
+Why on earth does installing cummerbund require a goddamn **MySQL** client?!
+This is completely nuts.
+
+Ran into a giant pile of inscrutable errors even after installing all these
+bananas dependencies. Eventually tracked it down to the R version shipped in
+the Ubuntu package repository being too out of date to work with some of the
+required packages. I hate volatile software. Installed a newer version of
+R with [this guide](https://www.digitalocean.com/community/tutorials/how-to-install-r-on-ubuntu-18-04).
+
+Finally managed to get cummerbund working and started graphing stuff. It mostly
+works, but my graphs don't really look quite like theirs. Need to ask the
+professor about this.
+
+In the mean time, played around with using gnuplot to plot the data instead of
+R. Turned out to be not too bad, since cuffdiff already dumps its output in
+a textual format. Example of the plot comparing the expression levels of the
+various genes:
+
+ set logscale
+ unset key
+ plot "gene_exp.diff" using \
+ "value_1":"value_2" lt 3 pt 1 lw 1, \
+ x+(0.5*x) lt -1 lw 1 dt 2, \
+ x-(0.5*x) lt -1 lw 1 dt 2
+
+I also played around with adding some nicer default `linetype`s to my
+`~/.gnuplot` using colors from ColorBrewer. Fairly happy with the result so
+far, but I'll need to play around with them more over time to see if they hold
+up.