New git repo because I restructed my files then RStudio got angry

Lesson: be more organised or put up with the file structure you
have at the moment....
Made names more consistent

got rid off all the '.' in names and replaced with
underscore because it looks less ugly and confused
if everything is consistent
Adjusted data loading

File structure changes and improvement of perl script
required changes in the acquisition of data
Select for perfect hits in the array data

perfect hits have an e value of 0. I used that to
select the contigs to analyse this time.

Also realised that the de_duplicate data.frame was
actually unnecessary the subset of mito_contigs
would also have the correct number of names to allow
the me to add the names to the contigs.
Day and night was wrong

Spoke with Nick McGlincy and he said that the 1 or 2
stands for night or day rather than first collection
second collection as I initially thought. So my
circadian graphs have been wrong all along...
Merge branch 'perfhit_analysis'

Completed the selecting for perfect hits code

perfect hit selection is ready to be in master code
Configured output for perfect hit analysis

am going to remove the other bar graph - they aren't
interesting anymore
Cleaning up comments and white space
Adjusted custom colour pallete
Adjusted the cut off for tidal filtered genes

the analysis didn't turn up anything particularly
interesting.

I should test for significant change on all of them
and only show those that have presumably t test?
Adjusted timecourse

Played with the levels of whole array to try and get
a sensible time course, but the way that it was
sampled can't have both tidal and circadian time
properly represented
Started rrnL free data.frame
Code for doing t-test

Can now used significance to graph
Moved filtering and t-test to 4_do.R

The filtering and t-testing should be in do and
factored out into a function
Adjusted variable names and comments

corrected some missed name changes and made the
comments more compact around the filtering code
Created stat_summary function

factored the creation of statistical summary of the
experiment out to a function to make 4_do.R easier to
understand
Created a t-test function

factored out the t-test code into a function
Created another function file

This function file will have all the messy stuff from
2_clean.R in as functions to make things more logical
and pretty
Created renaming function

factored out the repetitive renaming of the seperate
dataframes for each timepoint.

couldn't factor it more because selecting the correct
columns is intensive and difficult to loop
Adjusting to make renaming function work