inst/scripts/analysis/plots/backbone_geometry/rama_by_chi1.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(viridis)


library(ggplot2)


library(plyr)


feature_analyses <- c(feature_analyses, methods::new("FeaturesAnalysis",
id = "rama_by_chi1",
author = "Matthew O'Meara",
brief_description = "Ramachandran plots conditional on the first sidechain torsional angle",
feature_reporter_dependencies = c("ResidueFeatures", "ProteinBackboneTorsionAngleFeatures", "ResidueSecondaryStructureFeatures", "PdbDataFeatures"),
run=function(self, sample_sources, output_dir, output_formats){


sele <-"
SELECT
	res.name3 AS res_type,
	CASE
-- figure out which is gauche+, gauche- and trans
		WHEN 0 < res_dofs.chi1 AND res_dofs.chi1 < 120 THEN 'chi1 60'
		WHEN -120 < res_dofs.chi1 AND res_dofs.chi1 < 0 THEN 'chi1 -60'
	  ELSE 'chi1 180' END AS chi1_bin,
	bb.phi, bb.psi
FROM
	residues AS res,
	residue_pdb_confidence AS res_conf,
	protein_residue_conformation AS res_dofs,
	protein_backbone_torsion_angles AS bb
WHERE
	res_conf.struct_id = res.struct_id AND res_conf.residue_number = res.resNum AND
	res_conf.max_temperature < 30 AND
	res_dofs.struct_id = res.struct_id AND res_dofs.seqpos == res.resNum AND
	bb.struct_id = res.struct_id AND bb.resNum == res.resNum;"

f <- query_sample_sources(sample_sources, sele)

f <- ddply(
	f, .(sample_source, res_type, chi1_bin),
	transform, counts = length(sample_source))

plot_parts <- list(
	theme_bw(),
	theme(panel.background=element_rect(fill="#00007F", color="#00007F")),
	stat_density2d(
		aes(x=phi, y=psi, fill=..density..), geom="tile", contour=FALSE),
	geom_indicator(aes(indicator=counts), colour="white", group=1),
	coord_equal(ratio=1),
	scale_x_continuous(expression(paste("phi Angle (Degrees)", sep="")), limits=c(-180, 180)),
	scale_y_continuous(expression(paste("psi Angle (Degrees)", sep="")), limits=c(-180, 180)),
	scale_fill_viridis('Density'),
	theme(legend.position="bottom", legend.direction="horizontal"))


narrow_output_formats <- transform(output_formats, width=height)

d_ply(f, .(sample_source, res_type, chi1_bin), function(sub_f){
	if(nrow(sub_f) < 5) {
		print("skipping this group:")
		print(summary(sub_f))
		return()
	}

	res_type <- as.character(sub_f[1, c("res_type")])
	chi1_bin_numeric <- as.numeric(sub_f[1, c("chi1_bin")])
	chi1_bin_character <- as.character(sub_f[1, c("chi1_bin")])
	ss_id <- as.character(sub_f[1, c("sample_source")])
	sample_source <- sample_sources[sample_sources$sample_source == ss_id,]
	sub_plot_id <- paste(
		"ramachandran_res-", res_type, "_chi1-", chi1_bin_numeric, "_ssid", ss_id,
		sep="")
	ggplot(data=sub_f) + plot_parts +
		ggtitle(paste(
			"Backbone Torsion Angles Res: ", res_type, " ",
			chi1_bin_character, " B-Factor < 30\nSample Source: ",
			ss_id, sep=""))
	save_plots(self, sub_plot_id, sample_source, output_dir, narrow_output_formats)
})


})) # end FeaturesAnalysis