inst/scripts/analysis/plots/hbonds/hydroxyl_sites/hydroxyl_overview.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(viridis)
feature_analyses <- c(feature_analyses, methods::new("FeaturesAnalysis",
id = "hydroxyl_overview",
author = "Matthew O'Meara",
brief_description = "",
long_description = "
-----------------------------------------------------------------------
|A |E |I |
| | | |
| HXL OH chi | DON HXL AHDist | DON HXL AHD |
| | | |
| | | |
| | | |
| | | |
---------------------------------------------------------------------|
|B |F |J |
| | | |
| AHX OH chi | DON AHX AHDist | DON AHX AHD |
| | | |
| | | |
| | | |
| | | |
----------------------------------------------------------------------
|C |G |K |
| | | |
| HXL BA-Chi | ACC HXL AHDist | ACC HXL AHD |
| | | |
| | | |
| | | |
| | | |
|--------------------|-----------------------------------------------|
|D |H |L |
| | | |
| AHX BA-Chi | ACC AHX AHDist | ACC AHX AHD |
| | | |
| | | |
| | | |
| | | |
|---------------------------------------------------------------------
",
feature_reporter_dependencies = c("ResidueFeatures", "HBondFeatures"),
run=function(self, sample_sources, output_dir, output_formats){
panelsAB <- function(narrow_output_formats){
# both donotes and accepts, where both partners are neither patner
# is ASN, IMD, IME, HXL, AHX make sure the hydrogen is well placed
sele <- "
create index if not exists hbond_sites_struct_id_resNum on hbond_sites (struct_id, resNum );
create index if not exists hbonds_struct_id_don_id on hbonds ( struct_id, don_id );
create index if not exists hbonds_struct_id_acc_id on hbonds ( struct_id, acc_id );
SELECT
res_conf.chi2 AS chi2,
res_conf.chi3 AS chi3,
CASE main_don.HBCHemType
WHEN 'hbdon_HXL' THEN res_conf.chi2
WHEN 'hbdon_AHX' THEN res_conf.chi3 END AS chi,
main_don.HBChemType AS chem_type,
'chi' AS dof
FROM
hbond_sites AS main_don CROSS JOIN
hbond_sites_pdb AS main_don_pdb CROSS JOIN
hbonds AS main_as_don_hb CROSS JOIN
hbond_sites AS partner_acc CROSS JOIN
protein_residue_conformation AS res_conf
WHERE
main_don_pdb.struct_id = main_don.struct_id AND
main_don_pdb.site_id = main_don.site_id AND
main_don_pdb.heavy_atom_temperature < 30 AND
main_as_don_hb.struct_id = main_don.struct_id AND
main_as_don_hb.don_id = main_don.site_id AND
partner_acc.struct_id = main_as_don_hb.struct_id AND
partner_acc.site_id = main_as_don_hb.acc_id AND
partner_acc.HBChemType != 'hbacc_ASN' AND
partner_acc.HBChemType != 'hbacc_IMD' AND
partner_acc.HBChemType != 'hbacc_IME' AND
partner_acc.HBChemType != 'hbacc_HXL' AND
partner_acc.HBChemType != 'hbacc_AHX' AND
ABS(partner_acc.resNum - main_don.resNum) > 5 AND
res_conf.struct_id = main_don.struct_id AND
res_conf.seqpos = main_don.resNum;"
f <- query_sample_sources(sample_sources, sele)
f <- na.omit(f, method="r")
f$chi <- f$chi
dens <- estimate_density_1d_wrap(
f, c("sample_source", "chem_type"), "chi", xlim=c(-180, 180), adjust=.6)
summary(dens)
dens$chem_type <- factor(
dens$chem_type,
levels=c("hbdon_HXL", "hbdon_AHX", "hbacc_HXL", "hbacc_AHX"),
labels=c("hbdon_HXL", "hbdon_AHX", "hbacc_HXL", "hbacc_AHX"))
dens$dof <- 'chi'
plot_id <- "hydroxyl_overview_AB"
p <- ggplot(data=dens) + theme_bw() +
facet_grid(chem_type ~ dof, drop=F) +
# coord_equal(ratio=1) +
geom_line(aes(x=x, y=y*1000, colour=sample_source), show_guide=F) +
scale_x_continuous('Protein Chi (degrees)', limits=c(-180, 180), breaks=c(-120, -60, 0, 60, 120)) +
scale_y_continuous('Feature Density', limits=c(0, 9.5), breaks=c(0,2,4,6,8))
save_plots(self, plot_id, sample_sources, output_dir, narrow_output_formats)
}
panelsCD <- function(narrow_output_formats) {
sele <-"
SELECT
geom.chi,
geom.cosBAH,
acc_atoms.base_x AS abx, acc_atoms.base_y AS aby, acc_atoms.base_z AS abz,
acc_atoms.base2_x AS ab2x, acc_atoms.base2_y AS ab2y, acc_atoms.base2_z AS ab2z,
acc_atoms.atm_x AS ax, acc_atoms.atm_y AS ay, acc_atoms.atm_z AS az,
don_atoms.atm_x AS hx, don_atoms.atm_y AS hy, don_atoms.atm_z AS hz,
acc.HBChemType AS chem_type,
'chi' AS dof
FROM
hbond_geom_coords AS geom,
hbonds AS hb,
hbond_sites AS don,
hbond_sites AS acc,
hbond_sites_pdb AS don_pdb, hbond_sites_pdb AS acc_pdb,
hbond_site_atoms AS don_atoms,
hbond_site_atoms AS acc_atoms
WHERE
hb.struct_id = geom.struct_id AND hb.hbond_id = geom.hbond_id AND
hb.struct_id = don.struct_id AND hb.don_id = don.site_id AND
hb.struct_id = acc.struct_id AND hb.acc_id = acc.site_id AND
don_pdb.struct_id = hb.struct_id AND don_pdb.site_id = hb.don_id AND
don_pdb.heavy_atom_temperature < 30 AND
acc_pdb.struct_id = hb.struct_id AND acc_pdb.site_id = hb.acc_id AND
acc_pdb.heavy_atom_temperature < 30 AND
don_atoms.struct_id = hb.struct_id AND don_atoms.site_id = hb.don_id AND
acc_atoms.struct_id = hb.struct_id AND acc_atoms.site_id = hb.acc_id AND
ABS(don.resNum - acc.resNum ) > 5 AND
(acc.HBChemType == 'hbacc_HXL' OR acc.HBChemType == 'hbacc_AHX');"
f <- query_sample_sources(sample_sources, sele)
f <- transform(f,
cosvBAH = vector_dotprod(
vector_normalize(cbind(ax-(abx+ab2x)/2, ay-(aby+ab2y)/2, az-(abz+ab2z)/2)),
vector_normalize(cbind(hx-ax, hy-ay, hz-az))),
vBAchi = vector_dihedral(
cbind(ab2x, ab2y, ab2z), cbind((abx+ab2x)/2, (aby+ab2y)/2, (abz+ab2z)/2),
cbind(ax, ay, az), cbind(hx, hy, hz)))
#equal area projection
f <- transform(f,
capx = 2*sin(acos(cosvBAH)/2)*cos(vBAchi),
capy = 2*sin(acos(cosvBAH)/2)*sin(vBAchi))
capx_limits <- c(-1.5,1.5)
capy_limits <- c(-1.5,1.5)
max_BAH_angle = 110 # in degrees
abs_cap_limit <- 2*sin((max_BAH_angle*pi/180)/2)
capx_limits <- c(-abs_cap_limit, abs_cap_limit)
capy_limits <- c(-abs_cap_limit, abs_cap_limit)
plot_parts <- list(
theme_bw(),
theme(panel.background=element_rect(fill="#00007F", colour="#00007F")),
geom_raster(aes(x=x, y=y, fill=z), show_guide=F),
facet_grid(chem_type ~ dof),
polar_equal_area_grids_bw(),
coord_equal(ratio=1),
scale_fill_viridis("Density"),
scale_x_continuous('<spacer>', limits=capx_limits, breaks=c()),
scale_y_continuous('<spacer>', limits=capy_limits, breaks=c()),
theme(
# axis.text.x=element_blank(),
# axis.text.y=element_blank(),
# axis.title.x=element_blank(),
# axis.title.y=element_blank(),
axis.ticks.x = element_blank(),
axis.ticks.y = element_blank()))
dens <- estimate_density_2d(
f[f$sample_source == sample_sources$sample_source[1],],
c("chem_type"), "capx", "capy", n_pts=300)
dens$chem_type <- factor(
dens$chem_type,
levels=c("hbdon_HXL", "hbdon_AHX", "hbacc_HXL", "hbacc_AHX"),
labels=c("hbdon_HXL", "hbdon_AHX", "hbacc_HXL", "hbacc_AHX"))
dens$dof <- 'chi'
plot_id <- "hydroxyl_overview_CD"
ggplot(data=dens) +
theme_bw() +
theme(panel.background=element_rect(fill="#00007F", colour="#00007F")) +
geom_raster(aes(x=x, y=y, fill=z)) +
facet_grid(chem_type ~ dof, drop=F) +
polar_equal_area_grids_bw() +
coord_equal(ratio=1) +
scale_fill_viridis("Density") +
scale_x_continuous('<spacer>', limits=capx_limits, breaks=c()) +
scale_y_continuous('<spacer>', limits=capy_limits, breaks=c()) +
theme(
# axis.text.x=element_blank(),
# axis.text.y=element_blank(),
# axis.title.x=element_blank(),
# axis.title.y=element_blank(),
axis.ticks.x = element_blank(),
axis.ticks.y = element_blank())
save_plots(self, plot_id, sample_sources, output_dir, narrow_output_formats)
}
panelsEtoL <- function(narrow_output_formats) {
sele <-"
SELECT
geom.AHdist AS AHdist,
geom.cosAHD AS cosAHD,
don.HBChemType AS chem_type
FROM
hbonds AS hb,
hbond_geom_coords AS geom,
hbond_sites AS don, hbond_sites AS acc,
hbond_sites_pdb AS don_pdb, hbond_sites_pdb AS acc_pdb
WHERE
geom.struct_id = hb.struct_id AND geom.hbond_id = hb.hbond_id AND
don.struct_id = hb.struct_id AND don.site_id = hb.don_id AND
acc.struct_id = hb.struct_id AND acc.site_id = hb.acc_id AND
don_pdb.struct_id = hb.struct_id AND don_pdb.site_id = hb.don_id AND
don_pdb.heavy_atom_temperature < 30 AND
acc_pdb.struct_id = hb.struct_id AND acc_pdb.site_id = hb.acc_id AND
acc_pdb.heavy_atom_temperature < 30 AND
ABS(don.resNum - acc.resNum ) > 5 AND
(don.HBChemType == 'hbdon_HXL' OR don.HBChemType == 'hbdon_AHX')
UNION
SELECT
geom.AHdist,
geom.cosAHD,
acc.HBChemType AS chem_type
FROM
hbonds AS hb,
hbond_geom_coords AS geom,
hbond_sites AS don, hbond_sites AS acc,
hbond_sites_pdb AS don_pdb, hbond_sites_pdb AS acc_pdb
WHERE
geom.struct_id = hb.struct_id AND geom.hbond_id = hb.hbond_id AND
don.struct_id = hb.struct_id AND don.site_id = hb.don_id AND
acc.struct_id = hb.struct_id AND acc.site_id = hb.acc_id AND
don_pdb.struct_id = hb.struct_id AND don_pdb.site_id = hb.don_id AND
don_pdb.heavy_atom_temperature < 30 AND
acc_pdb.struct_id = hb.struct_id AND acc_pdb.site_id = hb.acc_id AND
acc_pdb.heavy_atom_temperature < 30 AND
ABS(don.resNum - acc.resNum ) > 5 AND
(acc.HBChemType == 'hbacc_HXL' OR acc.HBChemType == 'hbacc_AHX');"
f <- query_sample_sources(sample_sources, sele)
f <- na.omit(f, method="r")
dens_AHdist <- estimate_density_1d(
f, c("sample_source", "chem_type"),
"AHdist", weight_fun = radial_3d_normalization)
dens_AHdist$dof <- "AHdist"
dens_AHdist$chem_type <- factor(
dens_AHdist$chem_type,
levels=c("hbdon_HXL", "hbdon_AHX", "hbacc_HXL", "hbacc_AHX"),
labels=c("hbdon_HXL", "hbdon_AHX", "hbacc_HXL", "hbacc_AHX"))
plot_id <- "hydroxyl_overview_EtoH"
p <- ggplot(data=dens_AHdist) + theme_bw() +
facet_grid(chem_type ~ dof) +
geom_line(aes(x=x, y=y, colour=sample_source), show_guide=F) +
scale_y_continuous("FeatureDensity", limits=c(0,9.5), breaks=c(0,2,4,6,8)) +
scale_x_continuous(
expression(paste('A-H Dist. (', ring(A), ')')), limits=c(1.4,2.7), breaks=c(1.6, 1.9, 2.2, 2.5))
save_plots(self, plot_id, sample_sources, output_dir, narrow_output_formats)
f$AHD <- acos(f$cosAHD) * 180/pi
cdf_AHD <- compute_quantiles(
f, c("sample_source", "chem_type"), "AHD")
cdf_AHD$dof <- "AHD"
cdf_AHD$y <- 100 * cdf_AHD$probs
cdf_AHD$x <- cdf_AHD$quantiles
cdf_AHD$chem_type <- factor(
cdf_AHD$chem_type,
levels=c("hbdon_HXL", "hbdon_AHX", "hbacc_HXL", "hbacc_AHX"),
labels=c("Don Hydroxyl: S,T", "Don Aromatic Hydroxyl: Y", "Acc Hydroxyl: S,T", "Acc Aromatic Hydroxyl: Y"))
plot_id <- "hydroxyl_overview_ItoL"
p <- ggplot(data=cdf_AHD) + theme_bw() +
facet_grid(chem_type ~ dof, drop=F) +
geom_line(aes(x=x, y=y, colour=sample_source), show_guide=F) +
scale_y_continuous("Quantiles", limit=c(0,1), breaks=c(0,.25, .50, .75)) +
scale_x_continuous("AHD Angle (degrees)")
save_plots(self, plot_id, sample_sources, output_dir, narrow_output_formats)
}
narrow_output_formats <- output_formats
narrow_output_formats$width <- narrow_output_formats$width/3
})) # end FeaturesAnalysis
momeara/RosettaFeatures documentation built on May 23, 2019, 6:07 a.m.
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# -*- 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(viridis)
feature_analyses <- c(feature_analyses, methods::new("FeaturesAnalysis",
id = "hydroxyl_overview",
author = "Matthew O'Meara",
brief_description = "",
long_description = "
-----------------------------------------------------------------------
|A |E |I |
| | | |
| HXL OH chi | DON HXL AHDist | DON HXL AHD |
| | | |
| | | |
| | | |
| | | |
---------------------------------------------------------------------|
|B |F |J |
| | | |
| AHX OH chi | DON AHX AHDist | DON AHX AHD |
| | | |
| | | |
| | | |
| | | |
----------------------------------------------------------------------
|C |G |K |
| | | |
| HXL BA-Chi | ACC HXL AHDist | ACC HXL AHD |
| | | |
| | | |
| | | |
| | | |
|--------------------|-----------------------------------------------|
|D |H |L |
| | | |
| AHX BA-Chi | ACC AHX AHDist | ACC AHX AHD |
| | | |
| | | |
| | | |
| | | |
|---------------------------------------------------------------------
",
feature_reporter_dependencies = c("ResidueFeatures", "HBondFeatures"),
run=function(self, sample_sources, output_dir, output_formats){
panelsAB <- function(narrow_output_formats){
# both donotes and accepts, where both partners are neither patner
# is ASN, IMD, IME, HXL, AHX make sure the hydrogen is well placed
sele <- "
create index if not exists hbond_sites_struct_id_resNum on hbond_sites (struct_id, resNum );
create index if not exists hbonds_struct_id_don_id on hbonds ( struct_id, don_id );
create index if not exists hbonds_struct_id_acc_id on hbonds ( struct_id, acc_id );
SELECT
res_conf.chi2 AS chi2,
res_conf.chi3 AS chi3,
CASE main_don.HBCHemType
WHEN 'hbdon_HXL' THEN res_conf.chi2
WHEN 'hbdon_AHX' THEN res_conf.chi3 END AS chi,
main_don.HBChemType AS chem_type,
'chi' AS dof
FROM
hbond_sites AS main_don CROSS JOIN
hbond_sites_pdb AS main_don_pdb CROSS JOIN
hbonds AS main_as_don_hb CROSS JOIN
hbond_sites AS partner_acc CROSS JOIN
protein_residue_conformation AS res_conf
WHERE
main_don_pdb.struct_id = main_don.struct_id AND
main_don_pdb.site_id = main_don.site_id AND
main_don_pdb.heavy_atom_temperature < 30 AND
main_as_don_hb.struct_id = main_don.struct_id AND
main_as_don_hb.don_id = main_don.site_id AND
partner_acc.struct_id = main_as_don_hb.struct_id AND
partner_acc.site_id = main_as_don_hb.acc_id AND
partner_acc.HBChemType != 'hbacc_ASN' AND
partner_acc.HBChemType != 'hbacc_IMD' AND
partner_acc.HBChemType != 'hbacc_IME' AND
partner_acc.HBChemType != 'hbacc_HXL' AND
partner_acc.HBChemType != 'hbacc_AHX' AND
ABS(partner_acc.resNum - main_don.resNum) > 5 AND
res_conf.struct_id = main_don.struct_id AND
res_conf.seqpos = main_don.resNum;"
f <- query_sample_sources(sample_sources, sele)
f <- na.omit(f, method="r")
f$chi <- f$chi
dens <- estimate_density_1d_wrap(
f, c("sample_source", "chem_type"), "chi", xlim=c(-180, 180), adjust=.6)
summary(dens)
dens$chem_type <- factor(
dens$chem_type,
levels=c("hbdon_HXL", "hbdon_AHX", "hbacc_HXL", "hbacc_AHX"),
labels=c("hbdon_HXL", "hbdon_AHX", "hbacc_HXL", "hbacc_AHX"))
dens$dof <- 'chi'
plot_id <- "hydroxyl_overview_AB"
p <- ggplot(data=dens) + theme_bw() +
facet_grid(chem_type ~ dof, drop=F) +
# coord_equal(ratio=1) +
geom_line(aes(x=x, y=y*1000, colour=sample_source), show_guide=F) +
scale_x_continuous('Protein Chi (degrees)', limits=c(-180, 180), breaks=c(-120, -60, 0, 60, 120)) +
scale_y_continuous('Feature Density', limits=c(0, 9.5), breaks=c(0,2,4,6,8))
save_plots(self, plot_id, sample_sources, output_dir, narrow_output_formats)
}
panelsCD <- function(narrow_output_formats) {
sele <-"
SELECT
geom.chi,
geom.cosBAH,
acc_atoms.base_x AS abx, acc_atoms.base_y AS aby, acc_atoms.base_z AS abz,
acc_atoms.base2_x AS ab2x, acc_atoms.base2_y AS ab2y, acc_atoms.base2_z AS ab2z,
acc_atoms.atm_x AS ax, acc_atoms.atm_y AS ay, acc_atoms.atm_z AS az,
don_atoms.atm_x AS hx, don_atoms.atm_y AS hy, don_atoms.atm_z AS hz,
acc.HBChemType AS chem_type,
'chi' AS dof
FROM
hbond_geom_coords AS geom,
hbonds AS hb,
hbond_sites AS don,
hbond_sites AS acc,
hbond_sites_pdb AS don_pdb, hbond_sites_pdb AS acc_pdb,
hbond_site_atoms AS don_atoms,
hbond_site_atoms AS acc_atoms
WHERE
hb.struct_id = geom.struct_id AND hb.hbond_id = geom.hbond_id AND
hb.struct_id = don.struct_id AND hb.don_id = don.site_id AND
hb.struct_id = acc.struct_id AND hb.acc_id = acc.site_id AND
don_pdb.struct_id = hb.struct_id AND don_pdb.site_id = hb.don_id AND
don_pdb.heavy_atom_temperature < 30 AND
acc_pdb.struct_id = hb.struct_id AND acc_pdb.site_id = hb.acc_id AND
acc_pdb.heavy_atom_temperature < 30 AND
don_atoms.struct_id = hb.struct_id AND don_atoms.site_id = hb.don_id AND
acc_atoms.struct_id = hb.struct_id AND acc_atoms.site_id = hb.acc_id AND
ABS(don.resNum - acc.resNum ) > 5 AND
(acc.HBChemType == 'hbacc_HXL' OR acc.HBChemType == 'hbacc_AHX');"
f <- query_sample_sources(sample_sources, sele)
f <- transform(f,
cosvBAH = vector_dotprod(
vector_normalize(cbind(ax-(abx+ab2x)/2, ay-(aby+ab2y)/2, az-(abz+ab2z)/2)),
vector_normalize(cbind(hx-ax, hy-ay, hz-az))),
vBAchi = vector_dihedral(
cbind(ab2x, ab2y, ab2z), cbind((abx+ab2x)/2, (aby+ab2y)/2, (abz+ab2z)/2),
cbind(ax, ay, az), cbind(hx, hy, hz)))
#equal area projection
f <- transform(f,
capx = 2*sin(acos(cosvBAH)/2)*cos(vBAchi),
capy = 2*sin(acos(cosvBAH)/2)*sin(vBAchi))
capx_limits <- c(-1.5,1.5)
capy_limits <- c(-1.5,1.5)
max_BAH_angle = 110 # in degrees
abs_cap_limit <- 2*sin((max_BAH_angle*pi/180)/2)
capx_limits <- c(-abs_cap_limit, abs_cap_limit)
capy_limits <- c(-abs_cap_limit, abs_cap_limit)
plot_parts <- list(
theme_bw(),
theme(panel.background=element_rect(fill="#00007F", colour="#00007F")),
geom_raster(aes(x=x, y=y, fill=z), show_guide=F),
facet_grid(chem_type ~ dof),
polar_equal_area_grids_bw(),
coord_equal(ratio=1),
scale_fill_viridis("Density"),
scale_x_continuous('<spacer>', limits=capx_limits, breaks=c()),
scale_y_continuous('<spacer>', limits=capy_limits, breaks=c()),
theme(
# axis.text.x=element_blank(),
# axis.text.y=element_blank(),
# axis.title.x=element_blank(),
# axis.title.y=element_blank(),
axis.ticks.x = element_blank(),
axis.ticks.y = element_blank()))
dens <- estimate_density_2d(
f[f$sample_source == sample_sources$sample_source[1],],
c("chem_type"), "capx", "capy", n_pts=300)
dens$chem_type <- factor(
dens$chem_type,
levels=c("hbdon_HXL", "hbdon_AHX", "hbacc_HXL", "hbacc_AHX"),
labels=c("hbdon_HXL", "hbdon_AHX", "hbacc_HXL", "hbacc_AHX"))
dens$dof <- 'chi'
plot_id <- "hydroxyl_overview_CD"
ggplot(data=dens) +
theme_bw() +
theme(panel.background=element_rect(fill="#00007F", colour="#00007F")) +
geom_raster(aes(x=x, y=y, fill=z)) +
facet_grid(chem_type ~ dof, drop=F) +
polar_equal_area_grids_bw() +
coord_equal(ratio=1) +
scale_fill_viridis("Density") +
scale_x_continuous('<spacer>', limits=capx_limits, breaks=c()) +
scale_y_continuous('<spacer>', limits=capy_limits, breaks=c()) +
theme(
# axis.text.x=element_blank(),
# axis.text.y=element_blank(),
# axis.title.x=element_blank(),
# axis.title.y=element_blank(),
axis.ticks.x = element_blank(),
axis.ticks.y = element_blank())
save_plots(self, plot_id, sample_sources, output_dir, narrow_output_formats)
}
panelsEtoL <- function(narrow_output_formats) {
sele <-"
SELECT
geom.AHdist AS AHdist,
geom.cosAHD AS cosAHD,
don.HBChemType AS chem_type
FROM
hbonds AS hb,
hbond_geom_coords AS geom,
hbond_sites AS don, hbond_sites AS acc,
hbond_sites_pdb AS don_pdb, hbond_sites_pdb AS acc_pdb
WHERE
geom.struct_id = hb.struct_id AND geom.hbond_id = hb.hbond_id AND
don.struct_id = hb.struct_id AND don.site_id = hb.don_id AND
acc.struct_id = hb.struct_id AND acc.site_id = hb.acc_id AND
don_pdb.struct_id = hb.struct_id AND don_pdb.site_id = hb.don_id AND
don_pdb.heavy_atom_temperature < 30 AND
acc_pdb.struct_id = hb.struct_id AND acc_pdb.site_id = hb.acc_id AND
acc_pdb.heavy_atom_temperature < 30 AND
ABS(don.resNum - acc.resNum ) > 5 AND
(don.HBChemType == 'hbdon_HXL' OR don.HBChemType == 'hbdon_AHX')
UNION
SELECT
geom.AHdist,
geom.cosAHD,
acc.HBChemType AS chem_type
FROM
hbonds AS hb,
hbond_geom_coords AS geom,
hbond_sites AS don, hbond_sites AS acc,
hbond_sites_pdb AS don_pdb, hbond_sites_pdb AS acc_pdb
WHERE
geom.struct_id = hb.struct_id AND geom.hbond_id = hb.hbond_id AND
don.struct_id = hb.struct_id AND don.site_id = hb.don_id AND
acc.struct_id = hb.struct_id AND acc.site_id = hb.acc_id AND
don_pdb.struct_id = hb.struct_id AND don_pdb.site_id = hb.don_id AND
don_pdb.heavy_atom_temperature < 30 AND
acc_pdb.struct_id = hb.struct_id AND acc_pdb.site_id = hb.acc_id AND
acc_pdb.heavy_atom_temperature < 30 AND
ABS(don.resNum - acc.resNum ) > 5 AND
(acc.HBChemType == 'hbacc_HXL' OR acc.HBChemType == 'hbacc_AHX');"
f <- query_sample_sources(sample_sources, sele)
f <- na.omit(f, method="r")
dens_AHdist <- estimate_density_1d(
f, c("sample_source", "chem_type"),
"AHdist", weight_fun = radial_3d_normalization)
dens_AHdist$dof <- "AHdist"
dens_AHdist$chem_type <- factor(
dens_AHdist$chem_type,
levels=c("hbdon_HXL", "hbdon_AHX", "hbacc_HXL", "hbacc_AHX"),
labels=c("hbdon_HXL", "hbdon_AHX", "hbacc_HXL", "hbacc_AHX"))
plot_id <- "hydroxyl_overview_EtoH"
p <- ggplot(data=dens_AHdist) + theme_bw() +
facet_grid(chem_type ~ dof) +
geom_line(aes(x=x, y=y, colour=sample_source), show_guide=F) +
scale_y_continuous("FeatureDensity", limits=c(0,9.5), breaks=c(0,2,4,6,8)) +
scale_x_continuous(
expression(paste('A-H Dist. (', ring(A), ')')), limits=c(1.4,2.7), breaks=c(1.6, 1.9, 2.2, 2.5))
save_plots(self, plot_id, sample_sources, output_dir, narrow_output_formats)
f$AHD <- acos(f$cosAHD) * 180/pi
cdf_AHD <- compute_quantiles(
f, c("sample_source", "chem_type"), "AHD")
cdf_AHD$dof <- "AHD"
cdf_AHD$y <- 100 * cdf_AHD$probs
cdf_AHD$x <- cdf_AHD$quantiles
cdf_AHD$chem_type <- factor(
cdf_AHD$chem_type,
levels=c("hbdon_HXL", "hbdon_AHX", "hbacc_HXL", "hbacc_AHX"),
labels=c("Don Hydroxyl: S,T", "Don Aromatic Hydroxyl: Y", "Acc Hydroxyl: S,T", "Acc Aromatic Hydroxyl: Y"))
plot_id <- "hydroxyl_overview_ItoL"
p <- ggplot(data=cdf_AHD) + theme_bw() +
facet_grid(chem_type ~ dof, drop=F) +
geom_line(aes(x=x, y=y, colour=sample_source), show_guide=F) +
scale_y_continuous("Quantiles", limit=c(0,1), breaks=c(0,.25, .50, .75)) +
scale_x_continuous("AHD Angle (degrees)")
save_plots(self, plot_id, sample_sources, output_dir, narrow_output_formats)
}
narrow_output_formats <- output_formats
narrow_output_formats$width <- narrow_output_formats$width/3
})) # end FeaturesAnalysis
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