def panel4x4(fn0, fn1, fn2, fn3, fn_out):
single_size = plot_config.single_figure_size
sc.Figure(
str(single_size[0] * 150) + "px",
str(single_size[1] * 150) + "px",
sc.Panel(sc.SVG(fn0).scale(1.0).move(0, 0)),
sc.Text("A", 5, 25, size=plot_config.fontsize_xhuge, weight='bold'),
sc.Panel(sc.SVG(fn1).scale(1.0).move(single_size[0] * 150 / 2., 0)),
sc.Text("B",
single_size[0] * 150 / 2 + 5.,
25,
size=plot_config.fontsize_xhuge,
weight='bold'),
sc.Panel(sc.SVG(fn2).scale(1.0).move(0, single_size[1] * 150 / 2.)),
sc.Text("C",
5,
single_size[1] * 150 / 2. + 25,
size=plot_config.fontsize_xhuge,
weight='bold'),
sc.Panel(
sc.SVG(fn3).scale(1.0).move(single_size[0] * 150 / 2.,
single_size[1] * 150 / 2.)),
sc.Text("D",
single_size[0] * 150 / 2. + 5,
single_size[1] * 150 / 2. + 25,
size=plot_config.fontsize_xhuge,
weight='bold'),
).save(fn_out)
def plot_analysis(self, display=True):
figdir = set_figdir(verbose=False)
figure_name = f"{figdir}/{timestamp()}-analysis.svg"
fig_handles = [
self.plot_singular_vals(savefig=True, verbose=False,
display=False)[-1],
self.plot_eigs(savefig=True, verbose=False, display=False)[-1],
self.plot_power_spectrum(savefig=True,
verbose=False,
display=False)[-1]
]
svgs = []
for fig in fig_handles:
svgs.append(sc.SVG(fig + '.svg', fix_mpl=True))
os.remove(f"{fig}.svg")
sc.Figure(
sum(svg.width for svg in svgs), max([svg.height for svg in svgs]),
sc.Panel(svgs[0], sc.Text("(a)", 6, 16, size=11)).move(0, 0),
sc.Panel(svgs[1], sc.Text("(b)", 6, 16,
size=11)).move(svgs[0].width, 0),
sc.Panel(svgs[2],
sc.Text("(c)", 6, 16,
size=11)).move(svgs[0].width + svgs[1].width,
0)).save(figure_name)
if display:
IPython.display.display(IPython.display.SVG(figure_name))
def panel2x2(fn0, fn1, fn_out, single_size=plot_config.single_figure_size):
sc.Figure(
str(single_size[0] * 150) + "px",
str(single_size[1] * 80) + "px",
sc.Panel(sc.SVG(fn0).scale(1.0).move(0, 15)),
sc.Text("A",
4,
12,
size=plot_config.fontsize_large,
weight='bold',
font='serif'),
sc.Panel(sc.SVG(fn1).scale(1.0).move(single_size[0] * 150 / 2., 15)),
sc.Text("B",
single_size[0] * 150 / 2 + 4.,
12,
size=plot_config.fontsize_large,
weight='bold',
font='serif')).save(fn_out)
def make_multipanel_fig(FIGS, CAP_SIZE=14,\
fig_name="fig.svg",\
transparent=True, correc_factor=70., DPI=100.):
""" take a list of figures and make a multi panel plot"""
label = list(string.ascii_uppercase)[:len(FIGS)]
SIZE = []
for fig in FIGS:
SIZE.append(fig.get_size_inches())
width = np.max([s[0] for s in SIZE])
height = np.max([s[1] for s in SIZE])
LABELS, XCOORD, YCOORD, SCALE = [], [], [], []
for i in range(len(FIGS)):
ff = 'f.svg'
FIGS[i].savefig('/tmp/' + str(i) + '.svg',
format='svg',
transparent=transparent)
if translate_to_bitmap_if_too_big(FIGS[i], '/tmp/' + str(i) + '.svg'):
SCALE.append(.7)
else:
SCALE.append(1.)
LABELS.append(label[i])
XCOORD.append((i % 3) * width * correc_factor)
YCOORD.append(int(i / 3) * height * correc_factor)
PANELS = []
for i in range(len(FIGS)):
PANELS.append(sg.Panel(\
sg.SVG('/tmp/'+str(i)+'.svg').move(XCOORD[i],YCOORD[i]).scale(SCALE[i]),\
sg.Text(LABELS[i], 25, 20, size=22, weight='bold').move(\
XCOORD[i]-15,YCOORD[i]))\
)
sg.Figure(str((min(len(FIGS)%3,3))*inch_to_cm(width))+"cm",\
str(inch_to_cm(height)*(int(len(FIGS)/3.01)+1))+"cm",\
*PANELS).save(fig_name)
def put_list_of_figs_to_svg_fig(
FIGS,
fig_name="fig.svg",
initial_guess=True,
visualize=False,
export_as_png=False,
Props=None,
figsize=None,
fontsize=9,
SCALING_FACTOR=1.34, # needed to get the right cm size ...
with_top_left_letter=False,
transparent=True):
""" take a list of figures and make a multi panel plot"""
label = list(string.ascii_uppercase)[:len(FIGS)]
SIZE = []
for fig in FIGS:
if type(fig) == str:
SIZE.append([1., 1.])
else:
SIZE.append(fig.get_size_inches())
width = np.max([s[0] for s in SIZE])
height = np.max([s[1] for s in SIZE])
if Props is None:
LABELS, XCOORD, YCOORD = [], [], []
# saving as svg
for i in range(len(FIGS)):
LABELS.append(label[i])
XCOORD.append((i % 3) * width * 100)
YCOORD.append(int(i / 3) * height * 100)
XCOORD_LABELS,\
YCOORD_LABELS = XCOORD, YCOORD
else:
XCOORD, YCOORD = Props['XCOORD'],\
Props['YCOORD'],
if 'LABELS' in Props:
LABELS = Props['LABELS']
else:
LABELS = ['' for x in XCOORD]
if 'XCOORD_LABELS' in Props:
XCOORD_LABELS,\
YCOORD_LABELS = Props['XCOORD_LABELS'],\
Props['YCOORD_LABELS']
else:
XCOORD_LABELS,\
YCOORD_LABELS = XCOORD, YCOORD
LOCATIONS = []
for i in range(len(FIGS)):
if type(FIGS[i]) is str:
LOCATIONS.append(FIGS[i])
else:
LOCATIONS.append(os.path.join(gettempdir(), str(i) + '.svg'))
FIGS[i].savefig(LOCATIONS[-1],
format='svg',
transparent=transparent)
PANELS = []
for i in range(len(FIGS)):
PANELS.append(sg.Panel(\
sg.SVG(LOCATIONS[i]).move(XCOORD[i],YCOORD[i])))
for i in range(len(LABELS)):
PANELS.append(sg.Panel(\
sg.Text(LABELS[i], 15, 10,
size=fontsize, weight='bold').move(\
XCOORD_LABELS[i],YCOORD_LABELS[i]))\
)
sg.Figure("21cm", "29.7cm", *PANELS).scale(SCALING_FACTOR).save(fig_name)
# if figsize is None:
# sg.Figure("21cm", "29.7cm", *PANELS).save(fig_name)
# else:
# sg.Figure(str(inch2cm(figsize[0]*A0_format['width'])[0])+"cm",\
# str(inch2cm(figsize[1]*A0_format['height'])[0])+"cm",\
# *PANELS).scale(SCALING_FACTOR).save(fig_name)
if visualize:
os.system('open ' + fig_name) # works well with 'Gapplin' on OS-X
def multipanel_figure(graph_env,
FIGS,
X = None, Y = None, Labels=None,
LABELS = None, X_LABELS = None, Y_LABELS = None,
width=85.,# mm
height=None, # mm
grid=False,
autoposition=False,
SCALING_FACTOR = 1.34, fontsize=None, fontweight='bold',
export_to_png=False, bg='white',
fig_name='fig.svg'):
"""
"""
# building the figure matrix if not explicited
if type(FIGS) is mpl.figure.Figure:
FIGS = [[FIGS]]
elif type(FIGS) is list:
if (len(FIGS)>0) and (type(FIGS[0]) is mpl.figure.Figure):
FIGS = [FIGS]
elif (len(FIGS)>0) and (type(FIGS[0]) is str):
FIGS = [FIGS]
# else should be list of list
if autoposition:
X, Y = [], []
y = [0]
for i, lfig in enumerate(FIGS):
Y.append([np.max(y) for fig in lfig])
x = []
for fig in lfig:
if type(fig) is not str:
x.append(72.*fig.get_size_inches()[0])
y.append(72.*fig.get_size_inches()[1])
else:
x.append(120)
y.append(80)
X.append([0]+list(np.cumsum(x)))
y = [dy+Y[-1][0] for dy in y]
Y.append([np.max(y)])
print('X = ', X)
print('Y = ', Y)
if X is None:
X = [[0 for fig in lfig] for lfig in FIGS]
if Y is None:
Y = [[0 for fig in lfig] for lfig in FIGS]
if LABELS is None:
LABELS = [['' for fig in lfig] for lfig in FIGS]
if X_LABELS is None:
X_LABELS = X
if Y_LABELS is None:
Y_LABELS = Y
if height is None:
try:
height = np.max([50, Y[-1][-1]])*0.27 # TO BE SET UP
except IndexError:
height = 50
# size
if width=='single-column':
width = 85.
elif width=='one-and-a-half-column':
width = 114.
elif width=='one-column-and-a-half':
width = 114.
elif width=='double-column':
width = 174.
if fontsize is None:
fontsize = graph_env.fontsize+1
LOCATIONS, PANELS = [], []
for i, lfig in enumerate(FIGS):
LOCATIONS.append([])
for j, fig in enumerate(lfig):
if type(FIGS[i][j]) is str:
LOCATIONS[i].append(FIGS[i][j])
# 1.26625 -- NEW SCALING FACTOR
else:
LOCATIONS[i].append(os.path.join(gettempdir(), '%i_%i.svg' % (i,j)))
FIGS[i][j].savefig(LOCATIONS[i][j], format='svg',
transparent=graph_env.transparency)
PANELS.append(sg.Panel(sg.SVG(LOCATIONS[i][j]).move(X[i][j], Y[i][j])))
for i, labels in enumerate(LABELS):
for j, label in enumerate(labels):
if label!='':
PANELS.append(sg.Panel(sg.Text(label, 3, 10,
size=fontsize, weight=fontweight).move(\
X_LABELS[i][j],Y_LABELS[i][j])))
if grid:
sg.Figure("%.1fcm" % (width/10.), "%.1fcm" % (height/10.),
*PANELS, sg.Grid(40,40)).scale(SCALING_FACTOR).save(fig_name.replace('.png', '.svg'))
else:
sg.Figure("%.1fcm" % (width/10.), "%.1fcm" % (height/10.),
*PANELS).scale(SCALING_FACTOR).save(fig_name.replace('.png', '.svg'))
if fig_name.endswith('.png'):
export_as_png(fig_name.replace('.png', '.svg'), dpi=300, background=bg)
os.remove(fig_name.replace('.png', '.svg'))
print('[ok] removed %s' % fig_name.replace('.png', '.svg'))
elif export_to_png:
export_as_png(fig_name, dpi=300, background=bg)
def fsapt_analyze(lig_dir, mode, ene_type):
lig_name = os.path.basename(os.path.abspath(lig_dir))
matrix_dfs = []
outfiles = glob('%s/FSAPT*out' % lig_dir)
for of in outfiles:
df = _get_ene_matrix(of, ene_type)
if not df is None:
matrix_dfs.append(df)
all_df = pd.concat(matrix_dfs, axis=1)
mean_df = all_df.stack().groupby(level=[0, 1]).mean().unstack()
std_df = all_df.stack().groupby(level=[0, 1]).std().unstack()
if mode in ['prolig', 'proliglig']:
old_columns = mean_df.columns[:]
new_labels = []
numbering = []
for old_label in old_columns:
if old_label == 'Total':
new_labels.append('Total')
numbering.append(100000)
else:
labels = old_label.split('-')
if len(labels) == 2:
new_labels.append(''.join(labels))
numbering.append(float(labels[-1]))
elif len(labels) == 3:
new_labels.append('-'.join(labels[1:]))
numbering.append(0.5 *
(float(labels[-1]) + float(labels[-2])))
new_columns = [nl for _, nl in sorted(zip(numbering, new_labels))]
old_columns = [ol for _, ol in sorted(zip(numbering, old_columns))]
new_mean_df = pd.DataFrame()
new_std_df = pd.DataFrame()
for nc, oc in zip(new_columns, old_columns):
new_mean_df[nc] = mean_df[oc]
new_std_df[nc] = std_df[oc]
mean_df = new_mean_df
std_df = new_std_df
mean_anno = mean_df.applymap(lambda x: '%+.2f\n' % x)
std_anno = std_df.applymap(lambda x: r'+/-%.2f' % x)
all_anno = mean_anno + std_anno
matrix_svg = '%s/ene_matrix_%s.svg' % (lig_dir, ene_type)
plot_matrix(mean_df, all_anno, matrix_svg, mode, ene_type)
mean_df.to_csv('%s/ene_mean_%s_%s_%s.csv' %
(lig_dir, lig_name, mode, ene_type))
std_df.to_csv('%s/ene_std_%s_%s_%s.csv' %
(lig_dir, lig_name, mode, ene_type))
# Plot the ligand
dpi = 96
width = len(mean_df.columns) + 2
height = 4
ligmol = cs._RdkitMolBase.from_file('MD/%s/cmp_sybyl.mol2' % lig_name)
ligmol._init_atominfo(reset=False)
ligmol.charged_mol2file = 'MD/%s/cmp_sybyl.mol2' % lig_name
ligmol.get_noh_mol()
AllChem.Compute2DCoords(ligmol.noh_mol, canonOrient=True, bondLength=1.5)
drawer = rdMolDraw2D.MolDraw2DSVG(width * dpi, height * dpi)
opts = drawer.drawOptions()
opts.additionalAtomLabelPadding = 0.1
frag_dict, _ = fragment_mol(ligmol, 'L1')
for noha in ligmol.noh_mol.GetAtoms():
noh_idx = noha.GetIdx()
h_idx = ligmol.noh_to_h_atom_mapping[noh_idx]
frag_label = str(frag_dict[h_idx]['resid'])
if not 'L1-%02d' % int(frag_label) in mean_df.index:
continue
if noha.GetAtomicNum() == 6:
opts.atomLabels[noh_idx] = '%02d' % int(frag_label)
else:
elem = ligmol.GetAtomWithIdx(h_idx).GetProp(
'_TriposAtomType').split('.')[0]
opts.atomLabels[noh_idx] = '%s/%02d' % (elem, int(frag_label))
drawer.DrawMolecule(ligmol.noh_mol)
drawer.FinishDrawing()
svg = drawer.GetDrawingText().replace('svg:', '')
struct_svg = '%s/lig_frag_%s.svg' % (lig_dir, ene_type)
with open(struct_svg, 'w') as fh:
fh.writelines(svg)
# Consolidate the panels
if mode == 'prolig':
mat_title = 'Protein-Ligand %s Interaction' % ene_type.capitalize()
else:
mat_title = 'Ligand-Ligand %s Interaction' % ene_type.capitalize()
mat_title = sc.Panel(sc.Text(mat_title, size=24)).move(20, 20)
mat_panel = sc.Panel(sc.SVG(matrix_svg).scale(1.4)).move(0, 20)
struct_title = sc.Panel(sc.Text('Ligand %s' % lig_name,
size=24)).move(20,
dpi * len(mean_df) + 20)
struct_panel = sc.Panel(sc.SVG(struct_svg)).move(0,
dpi * len(mean_df) + 20)
final_figure = sc.Figure(dpi * width,
dpi * (len(mean_df) + height) + 40, mat_panel,
mat_title, struct_panel, struct_title)
final_name = '%s/%s_%s_%s' % (lig_dir, lig_name, mode, ene_type)
final_figure.save('%s.svg' % final_name)
os.system('convert -density 100 %s.svg %s.pdf' % (final_name, final_name))
os.system('rm -f %s %s' % (matrix_svg, struct_svg))
# Write pdb for pymol
inpdb = '%s/frame0/fsapt.pdb' % lig_dir
outpdb = '%s_pymol.pdb' % final_name
write_pymol_pdb(inpdb, outpdb, mean_df)
def composite(
fig_spec: FigureSpec,
memoize_panels: bool = False,
recompute_panels: bool = True,
delete_png: bool = True,
) -> None:
"""
Function that composites a figure from a FigureSpec.
Parameters
----------
fig_spec : FigureSpec
memoize_panels : bool
recompute_panels : bool
delete_png : bool
See the pubfig.compositor decorator for a description of the parameters.
Returns
-------
None
"""
import tempfile
svg_path = fig_spec.output_file
if isinstance(svg_path, str):
svg_path = Path(svg_path)
assert not svg_path.is_dir(), "The output file name you provided is a directory"
if svg_path.suffix != ".svg":
svg_path = svg_path.with_suffix(".svg")
svg_path = svg_path.expanduser()
if not svg_path.parent.exists():
svg_path.parent.mkdir(parents=True, exist_ok=True)
if memoize_panels:
panels_path = svg_path.parent / ".panels"
if not panels_path.exists():
panels_path.mkdir()
else:
panels_path = Path(tempfile.gettempdir())
panels = []
if fig_spec.plot_grid_every > 0:
panels.append(_generate_grid(fig_spec.figure_size, fig_spec.plot_grid_every, font_size=8))
auto_label = fig_spec.auto_label_options
label_generator = auto_label.label_generator(auto_label.first_char.text)
for name in fig_spec.panels._fields:
panel = getattr(fig_spec.panels, name)
assert isinstance(panel, Panel)
panel_elements = []
assert isinstance(panel.fig, (plt.Figure, VectorImage, RasterImage))
content_offset = _location_to_str(
panel.location.units or fig_spec.figure_size.units, panel.content_offset
)
if isinstance(panel, PanelFig):
svg = _get_panel_content(panels_path, panel, name, memoize_panels, recompute_panels)
panel_elements.append(svg.move(*content_offset))
elif isinstance(panel.fig, VectorImage):
scale = panel.scale or panel.fig.scale
print(f"Scaling vector image {panel.fig.file.absolute()} by {scale:.3f}")
panel_elements.append(panel.fig.svg.scale(scale).move(*content_offset))
elif isinstance(panel.fig, RasterImage):
img_size = panel.fig.img_size
scale = panel.scale or 1.
img = sc.Image(
img_size.units.to_px(img_size.width),
img_size.units.to_px(img_size.height),
f"{panel.fig.file}",
)
panel_elements.append(img.scale(scale).move(*content_offset))
else:
raise TypeError(f"Unknown type of panel content {type(panel.fig)} for panel {name}")
if panel.text is not None:
panel_text = [
sc.Text(
t.text,
*_location_to_str(fig_spec.figure_size.units, Location(t.x, t.y, panel.location.units)),
**t.kwargs
) for t in panel.text]
for t, pt in zip(panel_text, panel.text):
# Need separate loop because rotate doesn't return the Text Element
t.move(*content_offset).rotate(pt.angle)
panel_elements += panel_text
if panel.auto_label:
label = sc.Text(
next(label_generator),
*_location_to_str(
fig_spec.figure_size.units,
Location(auto_label.first_char.x, auto_label.first_char.y)
),
**auto_label.first_char.kwargs
)
panel_elements.append(label)
location = _location_to_str(fig_spec.figure_size.units, panel.location)
panels.append(sc.Panel(*panel_elements).move(*location))
fs = fig_spec.figure_size
sc.Figure(
f"{fs.units.to_px(fs.width):.2f}px",
f"{fs.units.to_px(fs.height):.2f}px",
*panels
).save(svg_path)
if fig_spec.generate_image != ImageType.none:
""" Taken from this shell script:
#!/bin/sh
# Convert all arguments (assumed SVG) to a TIFF acceptable to PLOS
# Requires Inkscape and ImageMagick 6.8 (doesn't work with 6.6.9)
for i in $@; do
BN=$(basename $i .svg)
inkscape --without-gui --export-png="$BN.png" --export-dpi 400 $i
convert -compress LZW -alpha remove $BN.png $BN.tiff
mogrify -alpha off $BN.tiff
rm $BN.png
done
"""
basename = f"{svg_path}"[:-4]
image_name = f"{basename}.png"
_run(f"inkscape --without-gui --export-png='{image_name}' --export-dpi {fig_spec.image_dpi} {svg_path}")
if fig_spec.generate_image == ImageType.tiff:
tiff_name = f"{basename}.tiff"
_run(f"convert -compress LZW -alpha remove {image_name} {tiff_name}")
_run(f"mogrify -alpha off {tiff_name}")
if delete_png:
_run(f"rm {image_name}")
image_name = tiff_name
_run(f"eog {image_name}")
def add_title(self, fig, title, y_pos=-0.2, w=None):
"""
`fig`: a plotly/svgutils Figure object, or the path of a png file.
`title`: figure title.
`w`: output image width in px.
"""
if isinstance(fig, str):
if not os.path.exists(fig):
print('File %s does exist!'%(fig))
return
if not os.path.splitext(os.path.abspath(fig))[-1]=='.png':
print('Only png image supported.')
return
im = Image.open(fig)
if w:
_w = w
else:
_w = self.output_width
_scalar = _w * 1.0 / im.width
svg_fig = sc.Figure(_w, ceil(_scalar * im.height),
sc.Image(
im.width,
im.height,
fig
).scale(_scalar)
)
fig = svg_fig
assert isinstance(fig, go.Figure) or isinstance(fig, sc.Figure)
# if input a plotly Figure object, convert it into a svg file first
title_txt = '%s%s '%(self.prefix, self.current_num) + title
if isinstance(fig, go.Figure):
# compute image size
if w:
_w = w
else:
_w = self.output_width
if not fig.layout.width is None:
_scalar = _w * 1.0 / fig.layout.width
else:
# default width is 700px
_scalar = _w * 1.0 / 700
if not fig.layout.height is None:
_h = fig.layout.height * _scalar
else:
# default height is 450px
_h = 450.0 * _scalar
title_annotation = go.layout.Annotation(
xref = 'paper',
yref = 'paper',
x = 0.5,
y = y_pos,
xanchor = 'center',
yanchor = 'top',
text = title_txt,
font = dict(
family = self.font_family,
size = self.font_size,
color = "#000000",
),
showarrow = False,
)
fig.update_layout(
width = _w,
height = _h,
annotations = list(fig.layout['annotations']) + [title_annotation],
)
# increasing counter number
self.current_num += 1
return fig
else:
# compute image size
if w:
_w = w
else:
_w = self.output_width
_scalar = _w * 1.0 / fig.width.value
_h = fig.height.value * _scalar + 25
if y_pos==-0.2:
text_y = _h - 5
else:
assert y_pos<=1 and y_pos>=0
text_y = int(_h*(1-y_pos))
# if w < default output width, add margin
if _w < self.output_width:
_outw = self.output_width
_move_x = int((_outw - _w) / 2)
else:
_outw = _w
_move_x = int((_outw - _w) / 2)
# add title
new_figure = sc.Figure(_outw, _h,
fig.scale(_scalar).move(_move_x, 0),
sc.Text(title_txt,
_outw / 2,
text_y,
anchor='middle',
size=self.font_size,
font=self.font_family,
)
)
# increasing counter number
self.current_num += 1
return new_figure