# -*- 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 = "rama_zoom_THR",
author = "Matthew O'Meara",
brief_description = "Ramachandran plots conditional on the first sidechain torsional angle for THR when chi1 is in the -60 degree bin",
feature_reporter_dependencies = c("ResidueFeatures", "ProteinBackboneTorsionAngleFeatures", "ResidueSecondaryStructureFeatures", "PdbDataFeatures"),
run=function(self, sample_sources, output_dir, output_formats){
sele <-"
SELECT
res.name3 AS res_type,
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 AND
res.name3 == 'THR' AND -120 < res_dofs.chi1 AND res_dofs.chi1 < 0 AND
-150 < bb.phi AND bb.phi < -100 AND
100 < bb.psi AND bb.psi < 150;"
phi_range <- c(-150, -100)
psi_range <- c(100, 150)
f <- query_sample_sources(sample_sources, sele)
f$chi1_bin <- "all"
narrow_output_formats <- transform(output_formats, width=height)
d_ply(f, .(sample_source, res_type, chi1_bin), function(sub_f){
if(nrow(sub_f) < 5) {
print("skipping this group:")
print(summary(sub_f))
return()
}
res_type <- as.character(sub_f[1, c("res_type")])
chi1_bin_numeric <- as.numeric(sub_f[1, c("chi1_bin")])
chi1_bin_character <- as.character(sub_f[1, c("chi1_bin")])
ss_id <- as.character(sub_f[1, c("sample_source")])
sub_plot_id <- paste(
"ramachandran_zoom_helix_region_res_truncated_peaks-", res_type, "_chi1-", chi1_bin_numeric, "_", ss_id,
sep="")
dens <- MASS::kde2d(sub_f$phi, sub_f$psi, n=300, h=1)
densdf <- data.frame(expand.grid(x=dens$x, y=dens$y), z=as.vector(dens$z))
densdf$counts <- nrow(sub_f)
ggplot(data=densdf) +
theme_bw() +
theme(panel.background=element_rect(fill="#00007F", colour="#00007F")) +
geom_tile(aes(x=x, y=y, fill=z)) +
geom_indicator(aes(indicator=counts), color="white", group=1) +
coord_equal(ratio=1) +
scale_fill_viridis('Density', limits=c(0, .01)) +
theme(legend.position="bottom", legend.direction="horizontal") +
ggtitle(paste(
"Backbone Torsion Angles Res (truncated peaks): ", res_type, " ",
chi1_bin_character, " B-Factor < 30\nSample Source: ",
ss_id, sep="")) +
scale_x_continuous(expression(paste("phi Angle (Degrees)", sep="")), limits=phi_range) +
scale_y_continuous(expression(paste("psi Angle (Degrees)", sep="")), limits=psi_range)
save_plots(self, sub_plot_id, sample_sources, output_dir, narrow_output_formats)
sub_plot_id <- paste(
"ramachandran_zoom_res-", res_type, "_chi1-", chi1_bin_numeric,"_", ss_id,
sep="")
ggplot(data=densdf) +
theme_bw() +
theme(panel.background=element_rect(fill="#00007F", colour="#00007F")) +
geom_tile(aes(x=x, y=y, fill=z)) +
geom_indicator(aes(indicator=counts), color="white", group=1) +
coord_equal(ratio=1) +
scale_fill_viridis("Density") +
theme(legend.position="bottom", legend.direction="horizontal") +
ggtitle(paste(
"Backbone Torsion Angles Res: ", res_type, " ",
chi1_bin_character, " B-Factor < 30\nSample Source: ",
ss_id, sep="")) +
scale_x_continuous(expression(paste("phi Angle (Degrees)", sep="")), limits=phi_range) +
scale_y_continuous(expression(paste("psi Angle (Degrees)", sep="")), limits=psi_range)
save_plots(self, sub_plot_id, sample_sources, output_dir, narrow_output_formats)
})
})) # end FeaturesAnalysis
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.