# -*- 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)
library(viridis)
feature_analyses <- c(feature_analyses, methods::new("FeaturesAnalysis",
id = "ramachandran_by_residue_type_and_secondary_structure_tight_kernel",
author = "Matthew O'Meara",
brief_description = "",
feature_reporter_dependencies = c("ResidueFeatures", "ProteinBackboneTorsionAngleFeatures", "ResidueSecondaryStructureFeatures", "PdbDataFeatures"),
run=function(self, sample_sources, output_dir, output_formats){
sele <-"
SELECT
res.name3 AS res_type,
ss.dssp,
bb.phi, bb.psi
FROM
residues AS res,
residue_pdb_confidence AS res_conf,
residue_secondary_structure AS ss,
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
ss.struct_id = res.struct_id AND ss.resNum == 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, dssp),
transform, counts = length(sample_source))
plot_parts <- list(
theme_bw(),
geom_raster(aes(x=x, y=y, fill=z)),
# geom_indicator(aes(indicator=counts), color="white", group=1),
coord_equal(ratio=1),
scale_x_continuous(expression(paste("phi Angle (Degrees)", sep=""))),
scale_y_continuous(expression(paste("psi Angle (Degrees)", sep=""))),
scale_fill_viridis("Density"),
theme(
legend.position="bottom",
legend.direction="horizontal",
panel.grid.major=element_blank(),
panel.grid.minor=element_blank(),
panel.background=element_rect(fill="#00007F")))
narrow_output_formats <- transform(output_formats, width=height)
d_ply(f, .(sample_source, res_type, dssp), function(sub_f){
if(nrow(sub_f) < 5) return()
res_type <- as.character(sub_f[1, c("res_type")])
dssp <- as.character(sub_f[1, c("dssp")])
ss_id <- as.character(sub_f[1, c("sample_source")])
sub_plot_id <- paste("ramachandran_res-", res_type, "_dssp-", dssp,"_", ss_id, sep="")
t <- system.time({
dens <- MASS::kde2d(sub_f$phi, sub_f$psi, n=500, h=5)
densdf <- data.frame(expand.grid(x=dens$x, y=dens$y), z=as.vector(dens$z)/max(dens$z))
# densdf$counts <- nrow(sub_f)
})
cat("estimate density ... ", as.character(round(t[3], 2)), "s\n", sep="")
ggplot(data=densdf) + plot_parts +
ggtitle(paste("Backbone Torsion Angles Res: ", res_type, " DSSP: ", dssp, " B-Factor < 30\nSample Source: ", ss_id, sep=""))
save_plots(self, sub_plot_id, sample_sources, output_dir, narrow_output_formats)
})
})) # end FeaturesAnalysis
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