inst/scripts/analysis/plots/hbonds/chi_sinBAH_polar_scatter_by_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)
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