# -*- 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)
library(plyr)
source("hbond_geo_dim_scales.R")
feature_analyses <- c(feature_analyses, methods::new("FeaturesAnalysis",
id = "chi_sinBAH_polar_scatter_by_chem_type",
author = "Matthew O'Meara",
brief_description = "",
feature_reporter_dependencies = c("HBondFeatures"),
run=function(self, sample_sources, output_dir, output_formats){
d_ply(sample_sources, .variables=("sample_source"), function(sample_source){
ss <- sample_source[1,"sample_source"]
sele <-"
SELECT
geom.AHdist, geom.cosBAH, geom.chi,
acc_site.HBChemType AS acc_chem_type,
don_site.HBChemType AS don_chem_type
FROM
hbond_geom_coords AS geom,
hbonds AS hbond,
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_source, sele)
f$acc_chem_type_name <- acc_chem_type_name_linear(f$acc_chem_type)
f$don_chem_type_name <- don_chem_type_name_linear(f$don_chem_type)
f <- na.omit(f, method="r")
#equal area projection
f <- transform(f,
capx = 2*sin(acos(cosBAH)/2)*cos(chi),
capy = 2*sin(acos(cosBAH)/2)*sin(chi))
plot_id = paste("hbond_sinBAH_eq_polar_scatter_by_chem_type", ss, sep="_")
ggplot(data=f) + theme_bw() +
polar_equal_area_grids_bw() +
geom_point(aes(x=capx, y=capy), size=.5) +
#stat_density2d(aes(x=capx, y=capy), size=.2) +
facet_grid(acc_chem_type_name ~ don_chem_type_name) +
ggtitle(paste("Hydrogen Bonds chi vs sinBAH Angles by Chemical Type\nEqual Coordinate Projection Sample Source: ", ss, sep="")) +
scale_x_continuous('', breaks=c(-1, 0, 1)) +
scale_y_continuous('', breaks=c(-1, 0, 1))
save_plots(self, plot_id, sample_source, output_dir, output_formats)
ddply(f, .(acc_chem_type_name, don_chem_type_name), function(df){
don_chem_type <- as.character(df$don_chem_type[1])
acc_chem_type <- as.character(df$acc_chem_type[1])
don_chem_type_name <- as.character(df$don_chem_type_name[1])
acc_chem_type_name <- as.character(df$acc_chem_type_name[1])
plot_id = paste("hbond_sinBAH_eq_polar_scatter", don_chem_type, acc_chem_type, ss, sep="_")
ggplot(data=df) + theme_bw() +
polar_equal_area_grids_bw() +
geom_point(aes(x=capx, y=capy), size=.5) +
#stat_density2d(aes(x=capx, y=capy), size=.2) +
ggtitle(paste("Hydrogen Bonds chi vs sinBAH Angles by ", don_chem_type_name, ", ", acc_chem_type_name, "\nEqual Coordinate Projection Sample Source: ", ss, sep="")) +
scale_x_continuous('2*sin(BAH/2) * cos(CHI)', breaks=c(-1, 0, 1)) +
scale_y_continuous('2*sin(BAH/2) * sin(CHI)', breaks=c(-1, 0, 1))
save_plots(self, plot_id, sample_source, output_dir, output_formats)
})
# #orthographic projection
# f <- transform(f,
# capx = sin(acos(cosBAH))*cos(chi),
# capy = sin(acos(cosBAH))*sin(chi))
#
#
# plot_id = paste("hbond_sinBAH_ortho_polar_scatter_by_chem_type", ss, sep="_")
# ggplot(data=f) + theme_bw() +
# geom_point(aes(x=capx, y=capy), size=.5) +
# #stat_density2d(aes(x=capx, y=capy), size=.2) +
# ggtitle(paste("Hydrogen Bonds chi vs sinBAH Angles by Chem Type\nOrthographic Projection Sample Source: ", ss, sep="")) +
# scale_x_continuous('sin(BAH) * cos(CHI)', breaks=c(-1, 0, 1)) +
# scale_y_continuous('sin(BAH) * sin(CHI)', breaks=c(-1, 0, 1))
# save_plots(self, plot_id, sample_source, output_dir, output_formats)
#
#
# ddply(f, .(acc_chem_type_name, don_chem_type_name), function(df){
# don_chem_type <- as.character(df$don_chem_type[1])
# acc_chem_type <- as.character(df$acc_chem_type[1])
# don_chem_type_name <- as.character(df$don_chem_type_name[1])
# acc_chem_type_name <- as.character(df$acc_chem_type_name[1])
#
# plot_id = paste("hbond_sinBAH_ortho_polar_scatter", don_chem_type, acc_chem_type, ss, sep="_")
# ggplot(data=df) + theme_bw() +
# geom_point(aes(x=capx, y=capy), size=.5) +
# #stat_density2d(aes(x=capx, y=capy), size=.2) +
# ggtitle(paste("Hydrogen Bonds chi vs sinBAH Angles ", don_chem_type_name, ", ", acc_chem_type_name, "\nOrthographic Projection Sample Source: ", ss, sep="")) +
# scale_x_continuous('sin(BAH) * cos(CHI)', breaks=c(-1, 0, 1)) +
# scale_y_continuous('sin(BAH) * sin(CHI)', breaks=c(-1, 0, 1))
# save_plots(self, plot_id, sample_source, output_dir, output_formats)
# })
})
})) # end FeaturesAnalysis
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