inst/scripts/analysis/plots/hbonds/geo_dim_1d/cosAHD_don_chem_type.R

In momeara/RosettaFeatures: Tools for analyzing macromolecular feature distributions with Rosetta

# -*- tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
# vi: set ts=2 noet:
#
# (c) Copyright Rosetta Commons Member Institutions.
# (c) This file is part of the Rosetta software suite and is made available under license.
# (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
# (c) For more information, see http://www.rosettacommons.org. Questions about this can be
# (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

library(ggplot2)


feature_analyses <- c(feature_analyses, methods::new("FeaturesAnalysis",
id = "cosAHD_don_chem_type",
author = "Matthew O'Meara",
brief_description = "",
feature_reporter_dependencies = c("HBondFeatures"),
run=function(self, sample_sources, output_dir, output_formats){


sele <-"
SELECT
	geom.cosAHD,
	don_site.HBChemType AS don_chem_type
FROM
	hbond_geom_coords AS geom,
	hbonds AS hb,
	hbond_sites AS don_site,
	hbond_sites AS acc_site,
	hbond_sites_pdb AS don_pdb, hbond_sites_pdb AS acc_pdb
WHERE
	hb.struct_id = geom.struct_id AND
	hb.hbond_id =  geom.hbond_id AND
	hb.struct_id = don_site.struct_id AND
	hb.don_id = don_site.site_id AND
	hb.struct_id = acc_site.struct_id AND
	hb.acc_id = acc_site.site_id AND
	don_pdb.struct_id = hb.struct_id AND
	don_pdb.site_id = hb.don_id AND
	don_pdb.heavy_atom_temperature < 30 AND
	acc_pdb.struct_id = hb.struct_id AND
	acc_pdb.site_id = hb.acc_id AND
	acc_pdb.heavy_atom_temperature < 30 AND
	abs( don_site.resNum - acc_site.resNum ) > 5;"

f <- query_sample_sources(sample_sources, sele)

# Order the plots better and give more descriptive labels
f$don_chem_type <- factor(f$don_chem_type,
	levels=c(
        	"hbdon_IMD", "hbdon_GDE", "hbdon_HXL", "hbdon_PBA",
		"hbdon_IME", "hbdon_GDH", "hbdon_AHX", "hbdon_IND",
		"hbdon_CXA", "hbdon_AMO"),
	labels = c(
        	"dIMD: h",   "dGDE: r", "dHXL: s,t", "dPBA: bb",
		"dIME: h",   "dGDH: r", "dAHX: y",   "dIND: w",
		"dCXA: n,q", "dAMO: k"))
f <- na.omit(f, method="r")

#coAHD goes from 0 to 1, where 1 is linear since there is significant
#density at 1, to accurately model a discontinuity, reflect the data
#across the right boundary, in computing the density esitmation
dens <- estimate_density_1d_reflect_boundary(
	data=f,
	ids = c("sample_source", "don_chem_type"),
	variable = "cosAHD",
	reflect_right=TRUE,
	right_boundary=1,
        adjust=.3)

plot_id = "cosAHD_don_chem_type"
p <- ggplot(data=dens) + theme_bw() +
	geom_line(aes(
        	x=180-acos(x)*180/pi, y=y, colour=sample_source)) +
	geom_indicator(aes(colour=sample_source, indicator=counts, group=sample_source)) +
	facet_wrap( ~ don_chem_type) +
	ggtitle(paste(
        	"Hydrogen Bonds AHD Angle ",
        	"by Donor Chemical Type; SeqSep > 5; BFact < 30\n",
        	"(normalized for equal volume per unit distance)",
        	sep="")) +
	scale_y_continuous(
        	"FeatureDensity",
        	limits=c(0,20), breaks=c(0,5,10,15)) +
	scale_x_continuous(
        	"Acceptor -- Hydrogen -- Donor (degrees)",
        	trans="reverse") +
	theme(legend.position=c(.58,.35)) +
	theme(legend.justification=c("left", "top"))

save_plots(self, plot_id, sample_sources, output_dir, output_formats)


})) # end FeaturesAnalysis