inst/scripts/analysis/plots/hbonds/abnormalities/fade_bump.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 = "fade_bump",
author = "Matthew O'Meara",
brief_description = "",
feature_reporter_dependencies = c("HBondFeatures"),
run=function(self, sample_sources, output_dir, output_formats){


sele <- "
SELECT
	geom.AHdist AS AHdist,
	don_site.HBChemType AS don_chem_type,
	acc_site.HBChemType AS acc_chem_type
FROM
	hbonds AS hbond,
	hbond_geom_coords AS geom,
	hbond_sites AS don_site,
	hbond_sites AS acc_site
WHERE
	hbond.struct_id = geom.struct_id AND hbond.hbond_id =  geom.hbond_id AND
	hbond.struct_id = don_site.struct_id AND hbond.don_id = don_site.site_id AND
	hbond.struct_id = acc_site.struct_id AND hbond.acc_id = acc_site.site_id;"

f <-  query_sample_sources(sample_sources, sele)

plot_parts <- list(
	theme_bw(),
	geom_line(aes(x, y, colour=sample_source), size=1.5),
	geom_indicator(aes(indicator=counts, colour=sample_source, group=sample_source)),
	labs(
		x=expression(paste('Acceptor -- Proton Distance (', ring(A), ')')),
		y="FeatureDensity"))

get_density <- function(data, ids){
	estimate_density_1d(
		data = data,
		ids = ids,
		variable = "AHdist",
		n_pts=300,
		weight_fun = radial_3d_normalization,
		histogram=TRUE)
}

################################
plot_id <- "fade_first_bump_all"
################################
dens <- get_density(f[1.8 <= f$AHdist & f$AHdist <= 2.0, ], c("sample_source"))
ggplot(data=dens) +
	geom_vline(xintercept = 1.9, colour="darkgray") +
	plot_parts +
	ggtitle("Hydrogen Bond A-H Distance First Fade Bump") +
	scale_x_continuous( breaks=c(1.85, 1.9, 1.95))
save_plots(self, plot_id, sample_sources, output_dir, output_formats)


##########################################
plot_id <- "fade_first_bump_don_chem_type"
##########################################
dens <- get_density(f[1.8 <= f$AHdist & f$AHdist <= 2.0, ], c("sample_source", "don_chem_type"))
ggplot(data=dens) +
	geom_vline(xintercept = 1.9, colour="darkgray") +
	plot_parts +
	facet_wrap(~don_chem_type) +
	ggtitle("Hydrogen Bond A-H Distance First Fade Bump by Donor Chem Type") +
	scale_x_continuous( breaks=c(1.85, 1.9, 1.95))
save_plots(self, plot_id, sample_sources, output_dir, output_formats)


##########################################
plot_id <- "fade_first_bump_acc_chem_type"
##########################################
dens <- get_density(f[1.8 <= f$AHdist & f$AHdist <= 2.0, ], c("sample_source", "acc_chem_type"))
ggplot(data=dens) +
	geom_vline(xintercept = 1.9, colour="darkgray") +
	plot_parts +
	facet_wrap(~acc_chem_type) +
	ggtitle("Hydrogen Bond A-H Distance First Fade Bump by Acceptor Chem Type") +
	scale_x_continuous( breaks=c(1.85, 1.9, 1.95))
save_plots(self, plot_id, sample_sources, output_dir, output_formats)


######################################
plot_id <- "fade_first_bump_chem_type"
######################################
dens <- get_density(f[1.8 <= f$AHdist & f$AHdist <= 2.0, ], c("sample_source", "don_chem_type", "acc_chem_type"))
ggplot(data=dens) +
	geom_vline(xintercept = 1.9, colour="darkgray") +
	plot_parts +
	facet_grid(don_chem_type ~ acc_chem_type) +
	ggtitle("Hydrogen Bond A-H Distance First Fade Bump by Chem Type") +
	scale_x_continuous( breaks=c(1.82, 1.9, 1.98))
save_plots(self, plot_id, sample_sources, output_dir, output_formats)


################################
plot_id <- "fade_last_bump_all"
################################
dens <- get_density(f[2.2 <= f$AHdist & f$AHdist <= 2.4, ], c("sample_source"))
ggplot(data=dens) +
	geom_vline(xintercept = 2.3, colour="darkgray") +
	plot_parts +
	ggtitle("Hydrogen Bond A-H Distance Last Fade Bump") +
	scale_x_continuous( breaks=c(2.25, 2.1, 2.45))
save_plots(self, plot_id, sample_sources, output_dir, output_formats)

#########################################
plot_id <- "fade_last_bump_don_chem_type"
#########################################
dens <- get_density(f[2.2 <= f$AHdist & f$AHdist <= 2.4, ], c("sample_source", "don_chem_type"))
ggplot(data=dens) +
	geom_vline(xintercept = 2.3, colour="darkgray") +
	plot_parts +
	facet_wrap(~don_chem_type) +
	ggtitle("Hydrogen Bond A-H Distance Last Fade Bump by Donor Chem Type") +
	scale_x_continuous( breaks=c(2.25, 2.1, 2.45))
save_plots(self, plot_id, sample_sources, output_dir, output_formats)


#########################################
plot_id <- "fade_last_bump_acc_chem_type"
#########################################
dens <- get_density(f[2.2 <= f$AHdist & f$AHdist <= 2.4, ], c("sample_source", "acc_chem_type"))
ggplot(data=dens) +
	geom_vline(xintercept = 2.3, colour="darkgray") +
	plot_parts +
	facet_wrap(~acc_chem_type) +
	ggtitle("Hydrogen Bond A-H Distance Last Fade Bump by Acceptor Chem Type") +
	scale_x_continuous( breaks=c(2.25, 2.1, 2.45))
save_plots(self, plot_id, sample_sources, output_dir, output_formats)


#####################################
plot_id <- "fade_last_bump_chem_type"
#####################################
dens <- get_density(f[2.2 <= f$AHdist & f$AHdist <= 2.4, ], c("sample_source", "don_chem_type", "acc_chem_type"))
ggplot(data=dens) +
	geom_vline(xintercept = 2.3, colour="darkgray") +
	plot_parts +
	facet_grid(don_chem_type ~ acc_chem_type) +
	ggtitle("Hydrogen Bond A-H Distance Last Fade Bump by Chem Type") +
	scale_x_continuous( breaks=c(2.22, 2.38))
save_plots(self, plot_id, sample_sources, output_dir, output_formats)


################################
plot_id <- "fade_range_bump_all"
################################
dens <- get_density(f[1.85 <= f$AHdist & f$AHdist <= 2.35, ], c("sample_source"))
ggplot(data=dens) +
#	geom_vline(xintercept = 1.9, colour="darkgray") +
#	geom_vline(xintercept = 2.3, colour="darkgray") +
	plot_parts +
	ggtitle("Hydrogen Bond A-H Distance Fade Range") +
	scale_x_continuous(breaks=c(1.9, 2.1, 2.3))
save_plots(self, plot_id, sample_sources, output_dir, output_formats)


##########################################
plot_id <- "fade_range_bump_don_chem_type"
##########################################
dens <- get_density(f[1.85 <= f$AHdist & f$AHdist <= 2.32, ], c("sample_source", "don_chem_type"))
ggplot(data=dens) +
	geom_vline(xintercept = 1.9, colour="darkgray") +
	geom_vline(xintercept = 2.3, colour="darkgray") +
	plot_parts +
	facet_wrap( ~ don_chem_type) +
	ggtitle("Hydrogen Bond A-H Distance Fade Range by Donor Chem Type") +
	scale_x_continuous( breaks=c(1.9, 2.3))
save_plots(self, plot_id, sample_sources, output_dir, output_formats)


##########################################
plot_id <- "fade_range_bump_acc_chem_type"
##########################################
dens <- get_density(f[1.85 <= f$AHdist & f$AHdist <= 2.35, ], c("sample_source", "acc_chem_type"))
ggplot(data=dens) +
	geom_vline(xintercept = 1.9, colour="darkgray") +
	geom_vline(xintercept = 2.3, colour="darkgray") +
	plot_parts +
	facet_wrap( ~ acc_chem_type) +
	ggtitle("Hydrogen Bond A-H Distance Fade Range by Acceptor Chem Type") +
	scale_x_continuous( breaks=c(1.9, 2.3))
save_plots(self, plot_id, sample_sources, output_dir, output_formats)


######################################
plot_id <- "fade_range_bump_chem_type"
######################################
dens <- get_density(f[1.85 <= f$AHdist & f$AHdist <= 2.35, ], c("sample_source", "don_chem_type", "acc_chem_type"))
ggplot(data=dens) +
	geom_vline(xintercept = 1.9, colour="darkgray") +
	geom_vline(xintercept = 2.3, colour="darkgray") +
	plot_parts +
	facet_grid(don_chem_type ~ acc_chem_type) +
	ggtitle("Hydrogen Bond A-H Distance Fade Range by Chem Type") +
	scale_x_continuous( breaks=c(1.9, 2.3))
save_plots(self, plot_id, sample_sources, output_dir, output_formats)


})) # end FeaturesAnalysis