Mostly various python plotting scripts. Quite a range including some old scripts which are rarely used. For internal reference only.
Require installation of NumPy, Matplotlib, SciPy and Pandas.
for plotting manual legend entries:
multiple_legend.py
multiple things, including loading multiple repeats of data into a 2D array for mean+sd analyses:
PLOT_1D_dens.py
loading multiple data sets into a single 1D array:
PLOT_msd_2D.py
combining csv contact files into one array in bash
get_average_from_csv.sh
get and average data PMF data as 1D arrays, put into a 2D array and average (as per https://doi.org/10.1021/acs.jctc.9b00548)
PLOT_PMF_average.py
count number of columns, and plot each one as a separate line according to a cmap. This is a nice general time series plotting script.
PLOT_flip_count_col.py
use pandas to load a data of unknown size, a big improvement over numpy
PLOT_pd_standard.py
some cool matrix stuff
RMSD_2D.py
aligning densities for pseduo density plots
PLOT_meta_heatmap.py
nice 2D array plot
PLOT_dens_2D.py
Using MDanalysis to read multiple files and write a density file (as per https://doi.org/10.1038/s41467-021-25242-x)
site_occupancy.py
example of glob being used for finding all files in dir by extenion
analyse_rmsf.py
awk script for summing columns
combine_to_av2.sh
summing all columns of a file - a useful replacement for awk
column_stats.py
getting averages with grep
get_res.py
plot residue contact maps (as per https://doi.org/10.7554/eLife.80988)
PLOT_contact.py
cylinder analysis in MDAnalysis - essentially a refined RDF analysis, as per https://doi.org/10.1101/2022.12.13.520211) Some nice MDAanalysis syntax used
cylinder_CLA.py
density plotting script - add arg for number of repeats. Currently POPE/POPG/CARD
full_make_density_plots.sh 3
converting from xy data (e.g. PCA 2D proj) to a 2D hist, including printing data for use in e.g. Prism
convert_xy_to_2D_hist.ipynb