def double_choropleth(gdf,
label_fn=lambda _: "",
Rt_col="Rt",
Rt_proj_col="Rt_proj",
titles=["Current $R_t$", "Projected $R_t$ (1 Week)"],
arrangement=(1, 2),
label_kwargs={},
mappable=sm):
""" plot two choropleths side-by-side based on multiple metrics """
gdf["pt"] = gdf["geometry"].centroid
fig, (ax1, ax2) = plt.subplots(*arrangement)
for (ax, title, col) in zip((ax1, ax2), titles, (Rt_col, Rt_proj_col)):
ax.grid(False)
ax.set_xticks([])
ax.set_yticks([])
ax.set_title(title, loc="left", fontdict=theme.label)
gdf.plot(color=[mappable.to_rgba(_) for _ in gdf[col]],
ax=ax,
edgecolors="black",
linewidth=0.5,
missing_kwds={
"color": theme.accent,
"edgecolor": "white"
})
if label_fn is not None:
for (_, row) in gdf.iterrows():
label = label_fn(row)
Rt_c, Rt_p = round(row[Rt_col], 2), round(row[Rt_proj_col], 2)
a1 = ax1.annotate(s=f"{label}{Rt_c}",
xy=list(row["pt"].coords)[0],
ha="center",
fontfamily=theme.note["family"],
color="white",
**label_kwargs)
a2 = ax2.annotate(s=f"{label}{Rt_p}",
xy=list(row["pt"].coords)[0],
ha="center",
fontfamily=theme.note["family"],
color="white",
**label_kwargs)
a1.set_path_effects(
[Stroke(linewidth=2, foreground="black"),
Normal()])
a2.set_path_effects(
[Stroke(linewidth=2, foreground="black"),
Normal()])
cbar_ax = fig.add_axes([0.95, 0.25, 0.01, 0.5])
cb = fig.colorbar(mappable=mappable, orientation="vertical", cax=cbar_ax)
cbar_ax.set_title("$R_t$", fontdict=theme.note)
return PlotDevice(fig)
def insert_miniglobe(ax,
fig,
extent=[-50, -41, -30, -22],
center=[-45, -15],
location=None,
box_color='red',
box_alpha=1,
box_edge_width=1):
# upper left: [0.13, 0.642, 0.2, 0.15]
# lower right: [0.7, 0.18, 0.2, 0.2]
#
if not location:
location = [0.75, 0.18, 0.2, 0.2]
sub_ax = fig.add_axes(location,
projection=ccrs.Orthographic(center[0], center[1]))
# Make a nice border around the inset axes.
effect = Stroke(linewidth=.1, foreground='black', alpha=0.5)
sub_ax.outline_patch.set_path_effects([effect])
sub_ax.coastlines(linewidth=0.00000001, edgecolor='k', alpha=.8)
sub_ax.stock_img()
extent_box = sgeom.box(extent[0], extent[2], extent[1], extent[3])
sub_ax.add_geometries([extent_box],
ccrs.PlateCarree(),
facecolor='bisque',
edgecolor=box_color,
linewidth=box_edge_width,
alpha=box_alpha)
return sub_ax
def __init__(self,
size=1,
extent=0.025,
label="",
loc=2,
ax=None,
pad=0.6,
borderpad=0.5,
ppad=0,
sep=4,
prop=None,
frameon=False,
colour='black',
**kwargs):
# size: length of bar in data units.
# extent: height of bar ends in axes units.
if loc == 'upper right':
loc = 1
elif loc == 'upper left':
loc = 2
elif loc == 'lower left':
loc = 3
elif loc == 'lower right':
loc = 4
if colour in ['w', 'white']:
fc = 'w' # Foreground colour.
ec = 'k' # Edge colour.
else:
fc = 'k'
ec = 'w'
trans = ax.get_xaxis_transform()
size_bar = matplotlib.offsetbox.AuxTransformBox(trans)
rectangle = Rectangle((0, 0), width=size, height=extent, fc=fc, ec=ec)
size_bar.add_artist(rectangle)
text = matplotlib.offsetbox.TextArea(label,
minimumdescent=False,
textprops={'color': fc})
path_effects = [
Stroke(linewidth=2, foreground=ec, alpha=0.75),
Normal()
]
text._text.set_path_effects(path_effects)
self.vpac = matplotlib.offsetbox.VPacker( \
children=[size_bar, text], align="center", pad=ppad, sep=sep)
matplotlib.offsetbox.AnchoredOffsetbox.__init__( \
self, loc, pad=pad, borderpad=borderpad, child=self.vpac,
prop=prop, frameon=frameon)
def display_map(f1_radiances_subset_reproj, utm_resampler, fname):
lons, lats = utm_resampler.area_def.get_lonlats()
crs = ccrs.PlateCarree()
extent = [np.min(lons), np.max(lons), np.min(lats), np.max(lats)]
u_padding = 0.25
l_padding = 1
padded_extent = [
np.min(lons) - u_padding,
np.max(lons) + u_padding,
np.min(lats) - u_padding,
np.max(lats) + l_padding
]
ax = plt.axes(projection=crs)
ax.set_extent(padded_extent)
ax.coastlines(resolution='50m', color='black', linewidth=1)
gridlines = ax.gridlines(draw_labels=True)
ax.imshow(f1_radiances_subset_reproj,
transform=crs,
extent=extent,
origin='upper',
cmap='gray')
# Create an inset GeoAxes showing the location
sub_ax = plt.axes([0.5, 0.66, 0.2, 0.2], projection=ccrs.PlateCarree())
sub_ax.set_extent([95, 145, -20, 10])
# Make a nice border around the inset axes.
effect = Stroke(linewidth=4, foreground='wheat', alpha=0.5)
sub_ax.outline_patch.set_path_effects([effect])
# Add the land, coastlines and the extent of the Solomon Islands.
sub_ax.add_feature(cartopy.feature.LAND)
sub_ax.coastlines()
extent_box = sgeom.box(extent[0], extent[2], extent[1], extent[3])
sub_ax.add_geometries([extent_box],
ccrs.PlateCarree(),
color='none',
edgecolor='blue',
linewidth=2)
plt.savefig(os.path.join(fp.path_to_plume_tracking_visualisations, 'maps',
fname),
bbox_inches='tight',
dpi=300)
plt.close()
def test_patheffect1():
ax1 = plt.subplot(111)
ax1.imshow([[1, 2], [2, 3]])
txt = ax1.annotate("test", (1., 1.), (0., 0),
arrowprops=dict(arrowstyle="->",
connectionstyle="angle3", lw=2),
size=20, ha="center",
path_effects=[withStroke(linewidth=3,
foreground="w")])
txt.arrow_patch.set_path_effects([Stroke(linewidth=5,
foreground="w"),
Normal()])
ax1.grid(True, linestyle="-")
pe = [withStroke(linewidth=3, foreground="w")]
for l in ax1.get_xgridlines() + ax1.get_ygridlines():
l.set_path_effects(pe)
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
# if "main" axes
if not kwargs.get("sharex"):
text = AnchoredText("PRELIMINARY",
loc="center",
frameon=False,
borderpad=0,
prop=dict(alpha=0.15,
fontsize=50,
rotation=30,
color="black"))
text.set_path_effects(
[Stroke(linewidth=3, foreground="white"),
Normal()])
text.set_zorder(1000)
self.add_artist(text)
def choropleth(gdf,
label_fn=lambda _: "",
col="Rt",
title="$R_t$",
label_kwargs={},
mappable=sm,
fig=None,
ax=None):
""" display choropleth of locations by metric """
gdf["pt"] = gdf["geometry"].centroid
if not fig:
fig, ax = plt.subplots()
ax.grid(False)
ax.set_xticks([])
ax.set_yticks([])
if title:
ax.set_title(title, loc="left", fontdict=theme.label)
gdf.plot(color=[mappable.to_rgba(_) for _ in gdf[col]],
ax=ax,
edgecolors="black",
linewidth=0.5,
missing_kwds={
"color": theme.accent,
"edgecolor": "white"
})
if label_fn is not None:
for (_, row) in gdf.iterrows():
label = label_fn(row)
value = round(row[col], 2)
ax.annotate(
s = f"{label}{value}",
xy = list(row["pt"].coords)[0],
ha = "center",
fontfamily = theme.note["family"],
color = "black", **label_kwargs,
fontweight = "semibold",
size = 12)\
.set_path_effects([Stroke(linewidth = 2, foreground = "white"), Normal()])
cbar_ax = fig.add_axes([0.90, 0.25, 0.01, 0.5])
cb = fig.colorbar(mappable=mappable, orientation="vertical", cax=cbar_ax)
cbar_ax.set_title("$R_t$", fontdict=theme.note)
return PlotDevice(fig)
def plot_global_hc_map(name_str, var, lakes_path, indir_lakedata):
# get region specific info from dictionary
if name_str == 'global_absolute':
levels = np.arange(-1e17, 1.1e17, 0.1e17)
elif name_str == 'global':
levels = np.arange(-1e19, 1.1e19, 0.1e19)
cb_orientation = 'horizontal'
path_lakes = lakes_path + name_str + '.shp'
# settings
clb_label = 'Joule'
title_str = name_str + ' heat content anomaly'
fig_name = 'Heat_content_' + name_str
cmap = 'RdBu_r' #, 'YlOrBr'
cmap, norm = mpu.from_levels_and_cmap(levels, cmap, extend='max')
lon, lat = get_lonlat(indir_lakedata)
LON, LAT = mpu.infer_interval_breaks(lon, lat)
# plotting
fig, ax = plt.subplots(1,
1,
figsize=(13, 8),
subplot_kw={'projection': ccrs.PlateCarree()})
ax.add_feature(ctp.feature.OCEAN, color='gainsboro')
ax.coastlines(color="grey")
# add the data to the map (more info on colormaps: https://matplotlib.org/users/colormaps.html)
h = ax.pcolormesh(LON, LAT, var, cmap=cmap, norm=norm)
# set grid lines
gl = ax.gridlines(crs=ccrs.PlateCarree(),
draw_labels=True,
linewidth=0.5,
color='gainsboro',
alpha=0.5)
gl.xlines = True
gl.xformatter = LONGITUDE_FORMATTER
gl.yformatter = LATITUDE_FORMATTER
gl.xlabels_bottom = None
gl.ylabels_right = None
effect = Stroke(linewidth=1.5, foreground='darkgray')
# set effect for main ax
ax.outline_patch.set_path_effects([effect])
# plot the colorbar
cbar = mpu.colorbar(h,
ax,
extend='max',
orientation=cb_orientation,
pad=0.05)
if cb_orientation == 'vertical':
cbar.ax.set_ylabel(clb_label, size=16)
elif cb_orientation == 'horizontal':
cbar.ax.set_xlabel(clb_label, size=16)
#ax.set_title(title_str, pad=10)
plotdir = '/home/inne/documents/phd/data/processed/isimip_lakeheat/plots/'
plt.savefig(plotdir + fig_name + '.png')
import matplotlib.dates as mdt
import matplotlib.font_manager as mfm
import matplotlib.patches as mpatch
import matplotlib.path as mpath
import matplotlib.pyplot as plt
import matplotlib.transforms as mtrans
import numpy as np
from matplotlib.patheffects import Normal, Stroke
from .cell import Cell, CellRow
from .gpf import pure_cmap
from .weathercode import WeatherCode
from .wxsymbols import wx_symbol_font
STROKE = [Stroke(linewidth=0.8, foreground='w'), Normal()]
ARROW_VER = [(0, -0.1), (0.66, -0.8), (0, 1), (-0.66, -0.8), (0, -0.1)]
ARROW_CODE = [
mpath.Path.MOVETO, mpath.Path.LINETO, mpath.Path.LINETO, mpath.Path.LINETO,
mpath.Path.CLOSEPOLY
]
ARROW = mpath.Path(ARROW_VER, ARROW_CODE)
temp_cmap = pure_cmap('temp')
fontpath = os.path.join(os.path.dirname(__file__), 'source.ttf')
source_font = mfm.FontProperties(fname=fontpath, size=6)
matplotlib.rc('font', family='HelveticaNeue', size=6)
ax = fig.add_subplot(4, 2, 6, xticks=[], yticks=[])
ax.imshow(I, cmap=cmap, origin="lower")
ax.text(
x,
y,
"Read me",
color="white",
transform=ax.transData,
bbox={
"facecolor": "black",
"edgecolor": "None",
"pad": 1,
"alpha": 0.75
},
)
ax = fig.add_subplot(4, 2, 7, xticks=[], yticks=[])
ax.imshow(I, cmap=cmap, origin="lower")
text = ax.text(x, y, "Read me", color="black", transform=ax.transData)
text.set_path_effects([Stroke(linewidth=1.5, foreground="white"), Normal()])
ax = fig.add_subplot(4, 2, 8, xticks=[], yticks=[])
ax.imshow(I, cmap=cmap, origin="lower")
text = ax.text(x, y, "Read me", color="white", transform=ax.transData)
text.set_path_effects([Stroke(linewidth=1.5, foreground="black"), Normal()])
plt.tight_layout()
plt.savefig("../../figures/typography/typography-legibility.pdf", dpi=600)
plt.show()
def Arrow(xi,
yi,
xf,
yf,
sc=20,
fc='#a2e3a2',
ec='black',
zo=0,
st='simple',
label=None,
lbHa='left',
lbVa='center',
lbPos='cen',
lbFs=10,
lbRot=0,
lbDx=0,
lbDy=0,
*args,
**kwargs):
"""
Draw arrow
==========
default arguments:
mutation_scale = sc
fc = fc
ec = ec
zorder = zo
arrowstyle = st
lbPos = {'cen', 'tip', 'tail'}
styles:
Curve - None
CurveB -> head_length=0.4,head_width=0.2
BracketB -[ widthB=1.0,lengthB=0.2,angleB=None
CurveFilledB -|> head_length=0.4,head_width=0.2
CurveA <- head_length=0.4,head_width=0.2
CurveAB <-> head_length=0.4,head_width=0.2
CurveFilledA <|- head_length=0.4,head_width=0.2
CurveFilledAB <|-|> head_length=0.4,head_width=0.2
BracketA ]- widthA=1.0,lengthA=0.2,angleA=None
BracketAB ]-[ widthA=1.0,lengthA=0.2,angleA=None,widthB=1.0,lengthB=0.2,angleB=None
Fancy fancy head_length=0.4,head_width=0.4,tail_width=0.4
Simple simple head_length=0.5,head_width=0.5,tail_width=0.2
Wedge wedge tail_width=0.3,shrink_factor=0.5
BarAB |-| widthA=1.0,angleA=None,widthB=1.0,angleB=None
"""
if not 'mutation_scale' in kwargs: kwargs['mutation_scale'] = sc
if not 'fc' in kwargs: kwargs['fc'] = fc
if not 'ec' in kwargs: kwargs['ec'] = ec
if not 'zorder' in kwargs: kwargs['zorder'] = zo
if not 'arrowstyle' in kwargs: kwargs['arrowstyle'] = st
if True: # makes arrow tips sharper
fa = FancyArrowPatch((xi, yi), (xf, yf),
shrinkA=False,
shrinkB=False,
path_effects=[Stroke(joinstyle='miter')],
*args,
**kwargs)
else:
fa = FancyArrowPatch((xi, yi), (xf, yf),
shrinkA=False,
shrinkB=False,
*args,
**kwargs)
gca().add_patch(fa)
if label:
if lbPos == 'cen':
xm = (xi + xf) / 2.0
ym = (yi + yf) / 2.0
if lbPos == 'tip':
xm, ym = xf, yf
if lbPos == 'tail':
xm, ym = xi, yi
gca().text(xm + lbDx,
ym + lbDy,
label,
ha=lbHa,
va=lbVa,
fontsize=lbFs,
rotation=lbRot)
return fa
def sbol_recombinase1(ax, type, num, start, end, prev_end, scale, linewidth,
opts):
""" SBOL recombinase site renderer - forward direction
"""
# Default parameters
color = (0, 0, 0)
color2 = (0, 0, 0)
start_pad = 0.0
end_pad = 0.0
x_extent = 6.0
y_extent = 6.0
linestyle = '-'
# Update default parameters if provided
if opts != None:
if 'start_pad' in list(opts.keys()):
start_pad = opts['start_pad']
if 'end_pad' in list(opts.keys()):
end_pad = opts['end_pad']
if 'x_extent' in list(opts.keys()):
x_extent = opts['x_extent']
if 'y_extent' in list(opts.keys()):
y_extent = opts['y_extent']
if 'linestyle' in list(opts.keys()):
linestyle = opts['linestyle']
if 'linewidth' in list(opts.keys()):
linewidth = opts['linewidth']
if 'scale' in list(opts.keys()):
scale = opts['scale']
if 'color' in list(opts.keys()):
color = opts['color']
if 'color2' in list(opts.keys()):
color2 = opts['color2']
# Check direction add start padding
final_end = end
final_start = prev_end
y_lower = -1 * y_extent / 2
y_upper = y_extent / 2
if start > end:
start = prev_end + end_pad + x_extent + linewidth
end = prev_end + end_pad
final_end = start + start_pad
color = color2
else:
start = prev_end + start_pad + linewidth
end = start + x_extent
final_end = end + end_pad
# Draw the site
p1 = Polygon([(start, y_lower), (start, y_upper), (end, 0)],
edgecolor=(0, 0, 0),
facecolor=color,
linewidth=linewidth,
zorder=11,
path_effects=[Stroke(joinstyle="miter")])
ax.add_patch(p1)
# Add a label if needed
if opts != None and 'label' in list(opts.keys()):
if final_start > final_end:
write_label(ax,
opts['label'],
final_end + ((final_start - final_end) / 2.0),
opts=opts)
else:
write_label(ax,
opts['label'],
final_start + ((final_end - final_start) / 2.0),
opts=opts)
# Return the final start and end positions to the DNA renderer
if final_start > final_end:
return prev_end, final_start
else:
return prev_end, final_end
def draw_outline(matplt_plot_obj, lw):
matplt_plot_obj.set_path_effects(
[Stroke(linewidth=lw, foreground='black'),
Normal()])
for x in np.linspace(0, 1, 20):
lw, color = x * 225, cmap(1 - x)
t = ax.text(
0.5,
0.45,
text,
size=size,
color="none",
weight="bold",
va="center",
ha="center",
family=family,
zorder=-lw,
)
t.set_path_effects([Stroke(linewidth=lw + 1, foreground="black")])
t = ax.text(
0.5,
0.45,
text,
size=size,
color="black",
weight="bold",
va="center",
ha="center",
family=family,
zorder=-lw + 1,
)
t.set_path_effects([Stroke(linewidth=lw, foreground=color)])
t = ax.text(
1.0,
def plot_region_hc_map(var, region_props, lakes_path, indir_lakedata):
# get region specific info from dictionary
extent = region_props['extent']
continent_extent = region_props['continent_extent']
name = region_props['name']
name_str = region_props['name_str']
ax_location = region_props['ax_location']
levels = region_props['levels']
fig_size = region_props['fig_size']
cb_orientation = region_props['cb_orientation']
path_lakes = lakes_path + name + '.shp'
# settings
clb_label = 'Joule'
title_str = name_str + ' heat content anomaly'
fig_name = 'Heat_content_' + name
cmap = 'YlOrBr'
cmap, norm = mpu.from_levels_and_cmap(levels, cmap, extend='max')
lon, lat = get_lonlat(indir_lakedata)
LON, LAT = mpu.infer_interval_breaks(lon, lat)
lakes = gpd.read_file(path_lakes)
# plotting
fig, ax = plt.subplots(1,
1,
figsize=fig_size,
subplot_kw={'projection': ccrs.PlateCarree()})
ax.add_feature(ctp.feature.OCEAN, color='gainsboro')
ax.coastlines(color="grey")
# add the data to the map (more info on colormaps: https://matplotlib.org/users/colormaps.html)
h = ax.pcolormesh(LON, LAT, var, cmap=cmap, norm=norm)
# load the lake shapefile
lakes.plot(ax=ax, edgecolor='gray', facecolor='none')
# set grid lines
gl = ax.gridlines(crs=ccrs.PlateCarree(),
draw_labels=True,
linewidth=0.5,
color='gainsboro',
alpha=0.5)
gl.xlines = True
gl.xformatter = LONGITUDE_FORMATTER
gl.yformatter = LATITUDE_FORMATTER
gl.xlabels_bottom = None
gl.ylabels_right = None
# set extent (in right way)
extent[1], extent[2] = extent[2], extent[1]
ax.set_extent(extent)
# create effect for map borders:
effect = Stroke(linewidth=1.5, foreground='darkgray')
# set effect for main ax
ax.outline_patch.set_path_effects([effect])
# Create an inset GeoAxes showing the location of the lakes region
#x0 y0 width height
sub_ax = fig.add_axes(ax_location, projection=ccrs.PlateCarree())
sub_ax.set_extent(continent_extent)
#lakes.plot(ax=sub_ax)
sub_ax.outline_patch.set_path_effects([effect])
extent_box = sgeom.box(extent[0], extent[2], extent[1], extent[3])
sub_ax.add_geometries([extent_box],
ccrs.PlateCarree(),
facecolor='none',
edgecolor='red',
linewidth=2)
# Add the land, coastlines and the extent of the inset axis
sub_ax.add_feature(cfeature.LAND, edgecolor='gray')
sub_ax.coastlines(color='gray')
extent_box = sgeom.box(extent[0], extent[2], extent[1], extent[3])
sub_ax.add_geometries([extent_box],
ccrs.PlateCarree(),
facecolor='none',
edgecolor='black',
linewidth=2)
# plot the colorbar
cbar = mpu.colorbar(h,
ax,
extend='max',
orientation=cb_orientation,
pad=0.05)
if cb_orientation == 'vertical':
cbar.ax.set_ylabel(clb_label, size=16)
elif cb_orientation == 'horizontal':
cbar.ax.set_xlabel(clb_label, size=16)
#ax.set_title(title_str, pad=10)
plotdir = '/home/inne/documents/phd/data/processed/isimip_lakeheat/plots/'
plt.savefig(plotdir + fig_name + '.png', dpi=500)
def main():
# Define the two coordinate systems with different ellipses.
wgs84 = ccrs.PlateCarree(globe=ccrs.Globe(datum='WGS84', ellipse='WGS84'))
sphere = ccrs.PlateCarree(
globe=ccrs.Globe(datum='WGS84', ellipse='sphere'))
# Define the coordinate system of the data we have from Natural Earth and
# acquire the 1:10m physical coastline shapefile.
geodetic = ccrs.Geodetic(globe=ccrs.Globe(datum='WGS84'))
dataset = cfeature.NaturalEarthFeature(category='physical',
name='coastline',
scale='10m')
# Create a Stamen map tiler instance, and use its CRS for the GeoAxes.
tiler = StamenTerrain()
fig = plt.figure()
ax = fig.add_subplot(1, 1, 1, projection=tiler.crs)
ax.set_title('The effect of incorrectly referencing the Solomon Islands')
# Pick the area of interest. In our case, roughly the Solomon Islands, and
# get hold of the coastlines for that area.
extent = [155, 163, -11.5, -6]
ax.set_extent(extent, geodetic)
geoms = list(dataset.intersecting_geometries(extent))
# Add the Stamen aerial imagery at zoom level 7.
ax.add_image(tiler, 7)
# Transform the geodetic coordinates of the coastlines into the two
# projections of differing ellipses.
wgs84_geoms = [
geom_transform(transform_fn_factory(wgs84, geodetic), geom)
for geom in geoms
]
sphere_geoms = [
geom_transform(transform_fn_factory(sphere, geodetic), geom)
for geom in geoms
]
# Using these differently referenced geometries, assume that they are
# both referenced to WGS84.
ax.add_geometries(wgs84_geoms, wgs84, edgecolor='white', color='none')
ax.add_geometries(sphere_geoms, wgs84, edgecolor='gray', color='none')
# Create a legend for the coastlines.
legend_artists = [
Line([0], [0], color=color, linewidth=3) for color in ('white', 'gray')
]
legend_texts = ['Correct ellipse\n(WGS84)', 'Incorrect ellipse\n(sphere)']
legend = ax.legend(legend_artists,
legend_texts,
fancybox=True,
loc='lower left',
framealpha=0.75)
legend.legendPatch.set_facecolor('wheat')
# Create an inset GeoAxes showing the location of the Solomon Islands.
sub_ax = fig.add_axes([0.7, 0.625, 0.2, 0.2],
projection=ccrs.PlateCarree())
sub_ax.set_extent([110, 180, -50, 10], geodetic)
# Make a nice border around the inset axes.
effect = Stroke(linewidth=4, foreground='wheat', alpha=0.5)
sub_ax.outline_patch.set_path_effects([effect])
# Add the land, coastlines and the extent of the Solomon Islands.
sub_ax.add_feature(cfeature.LAND)
sub_ax.coastlines()
extent_box = sgeom.box(extent[0], extent[2], extent[1], extent[3])
sub_ax.add_geometries([extent_box],
ccrs.PlateCarree(),
color='none',
edgecolor='blue',
linewidth=2)
plt.show()
def sbol_recombinase2(ax, type, num, start, end, prev_end, scale, linewidth,
opts):
""" SBOL recombinase site renderer - reverse direction
"""
# Default parameters
color = (0, 0, 0)
color2 = (0, 0, 0)
start_pad = 0.0
end_pad = 0.0
x_extent = 6.0
y_extent = 6.0
linestyle = '-'
# Update default parameters if provided
if opts != None:
if 'start_pad' in list(opts.keys()):
start_pad = opts['start_pad']
if 'end_pad' in list(opts.keys()):
end_pad = opts['end_pad']
if 'x_extent' in list(opts.keys()):
x_extent = opts['x_extent']
if 'y_extent' in list(opts.keys()):
y_extent = opts['y_extent']
if 'linestyle' in list(opts.keys()):
linestyle = opts['linestyle']
if 'linewidth' in list(opts.keys()):
linewidth = opts['linewidth']
if 'scale' in list(opts.keys()):
scale = opts['scale']
if 'color' in list(opts.keys()):
color = opts['color']
if 'color2' in list(opts.keys()):
color2 = opts['color2']
else:
if 'color' in list(opts.keys()):
r2 = float(color[0]) / 2
g2 = float(color[1]) / 2
b2 = float(color[2]) / 2
color2 = (r2, g2, b2)
# Check direction add start padding
final_end = end
final_start = prev_end
y_lower = -1 * y_extent / 2
y_upper = y_extent / 2
if start > end:
start = prev_end + end_pad + x_extent + linewidth
end = prev_end + end_pad
final_end = start + start_pad
temp = color
color = color2
color2 = temp
else:
start = prev_end + start_pad + linewidth
end = start + x_extent
final_end = end + end_pad
# Draw the site
p1 = Polygon([(start, y_lower), (start, y_upper), (end, 0)],
edgecolor=(0, 0, 0),
facecolor=color,
linewidth=linewidth,
zorder=11,
path_effects=[Stroke(joinstyle="miter")])
midpoint = (end + start) / 2
hypotenuse = math.sqrt((y_extent / 2)**2 + (x_extent)**2)
hypotenuse2 = hypotenuse / 2
cosineA = (y_extent / 2) / hypotenuse
f = hypotenuse2 * cosineA
p2 = Polygon([(midpoint, -1 * f), (midpoint, f), (end, 0)],
edgecolor=(0, 0, 0),
facecolor=color2,
linewidth=linewidth,
zorder=12,
path_effects=[Stroke(joinstyle="miter")])
ax.add_patch(p1)
ax.add_patch(p2)
# Add a label if needed
if opts != None and 'label' in list(opts.keys()):
if final_start > final_end:
write_label(ax,
opts['label'],
final_end + ((final_start - final_end) / 2.0),
opts=opts)
else:
write_label(ax,
opts['label'],
final_start + ((final_end - final_start) / 2.0),
opts=opts)
# Return the final start and end positions to the DNA renderer
if final_start > final_end:
return prev_end, final_start
else:
return prev_end, final_end
def promoter_region(ax, type, num, start, end, prev_end, scale, linewidth,
opts):
# Default parameters - these can be added to, but we usually use this style (probably should simplify in future)
y_offset = 0.0
color_35 = (0.5, 0.5, 0.5)
color_10 = (0.5, 0.5, 0.5)
color_connector = (0, 0, 0)
linewidth_connector = 2.0
len_35 = 4
len_10 = 2
y_extent = 4.0
# Update default parameters if provided
if opts != None:
if 'y_extent' in opts.keys():
y_extent = opts['y_extent']
if 'y_offset' in opts.keys():
y_offset = opts['y_offset']
if 'linewidth' in opts.keys():
linewidth = opts['linewidth']
if 'color_35' in opts.keys():
color_35 = opts['color_35']
if 'color_10' in opts.keys():
color_10 = opts['color_10']
if 'color_connector' in opts.keys():
color_connector = opts['color_connector']
if 'linewidth_connector' in opts.keys():
linewidth_connector = opts['linewidth_connector']
if 'len_35' in opts.keys():
len_35 = opts['len_35']
if 'len_10' in opts.keys():
len_10 = opts['len_10']
# Check direction (we don't use at moment)
fwd = True
if start > end:
fwd = False
# Draw the -35 site (from start to start + length of -35 site)
p35 = Polygon([(start, y_offset), (start, y_offset + y_extent),
(start + len_35, y_offset + y_extent),
(start + len_35, y_offset)],
edgecolor=(0, 0, 0),
facecolor=color_35,
linewidth=linewidth,
zorder=11,
path_effects=[Stroke(joinstyle="miter")])
ax.add_patch(p35)
# Draw the -10 site (from end-length of -10 site to end)
p10 = Polygon([(end - len_10, y_offset),
(end - len_10, y_offset + y_extent),
(end, y_offset + y_extent), (end, y_offset)],
edgecolor=(0, 0, 0),
facecolor=color_10,
linewidth=linewidth,
zorder=11,
path_effects=[Stroke(joinstyle="miter")])
ax.add_patch(p10)
l1 = Line2D([start + len_35, end - len_10],
[y_offset + (y_extent / 2.0), y_offset + (y_extent / 2.0)],
linewidth=linewidth_connector,
color=color_connector,
zorder=10)
ax.add_line(l1)
# Add a label if needed
if opts != None and 'label' in opts.keys():
if final_start > final_end:
dpl.write_label(ax,
opts['label'],
final_end + ((final_start - final_end) / 2.0),
opts=opts)
else:
dpl.write_label(ax,
opts['label'],
final_start + ((final_end - final_start) / 2.0),
opts=opts)
# Return the final start and end positions to the DNA renderer
return start, end
def plot_stations_map(self, **kwargs):
from matplotlib.transforms import offset_copy
import cartopy.crs as ccrs
from cartopy.mpl.gridliner import LONGITUDE_FORMATTER, LATITUDE_FORMATTER
from owslib.wms import WebMapService
from matplotlib.patheffects import Stroke
import cartopy.feature as cfeature
import shapely.geometry as sgeom
from matplotlib import pyplot as plt
from isp import ROOT_DIR
import os
os.environ["CARTOPY_USER_BACKGROUNDS"] = os.path.join(ROOT_DIR, "maps")
# MAP_SERVICE_URL = 'https://gis.ngdc.noaa.gov/arcgis/services/gebco08_hillshade/MapServer/WMSServer'
MAP_SERVICE_URL = 'https://www.gebco.net/data_and_products/gebco_web_services/2020/mapserv?'
# MAP_SERVICE_URL = 'https://gis.ngdc.noaa.gov/arcgis/services/etopo1/MapServer/WMSServer'
geodetic = ccrs.Geodetic(globe=ccrs.Globe(datum='WGS84'))
#layer = 'GEBCO_08 Hillshade'
layer ='GEBCO_2020_Grid'
#layer = 'shaded_relief'
epi_lat = kwargs.pop('latitude')
epi_lon = kwargs.pop('longitude')
name_stations = []
lat = []
lon = []
for name, coords in self.__stations_dict.items():
name_stations.append(name)
lat.append(float(coords[0]))
lon.append(float(coords[1]))
#
proj = ccrs.PlateCarree()
fig, ax = plt.subplots(1, 1, subplot_kw=dict(projection=proj), figsize=(16, 12))
self.mpf = MatplotlibFrame(fig)
xmin = min(lon)-4
xmax = max(lon)+4
ymin = min(lat)-4
ymax = max(lat)+4
extent = [xmin, xmax, ymin, ymax]
ax.set_extent(extent, crs=ccrs.PlateCarree())
try:
wms = WebMapService(MAP_SERVICE_URL)
ax.add_wms(wms, layer)
except:
ax.background_img(name='ne_shaded', resolution="high")
#geodetic_transform = ccrs.Geodetic()._as_mpl_transform(ax)
geodetic_transform = ccrs.PlateCarree()._as_mpl_transform(ax)
text_transform = offset_copy(geodetic_transform, units='dots', x=-25)
ax.scatter(lon, lat, s=12, marker="^", color='red', alpha=0.7, transform=ccrs.PlateCarree())
ax.plot(epi_lon, epi_lat, color='black', marker='*', markersize=8)
N=len(name_stations)
for n in range(N):
lon1=lon[n]
lat1 = lat[n]
name = name_stations[n]
ax.text(lon1, lat1, name, verticalalignment='center', horizontalalignment='right', transform=text_transform,
bbox=dict(facecolor='sandybrown', alpha=0.5, boxstyle='round'))
# Create an inset GeoAxes showing the Global location
#sub_ax = self.mpf.canvas.figure.add_axes([0.70, 0.75, 0.28, 0.28],
# projection=ccrs.PlateCarree())
sub_ax = self.mpf.canvas.figure.add_axes([0.70, 0.73, 0.28, 0.28], projection=ccrs.PlateCarree())
sub_ax.set_extent([-179.9, 180, -89.9, 90], geodetic)
# Make a nice border around the inset axes.
effect = Stroke(linewidth=4, foreground='wheat', alpha=0.5)
sub_ax.outline_patch.set_path_effects([effect])
# Add the land, coastlines and the extent .
sub_ax.add_feature(cfeature.LAND)
sub_ax.coastlines()
extent_box = sgeom.box(extent[0], extent[2], extent[1], extent[3])
sub_ax.add_geometries([extent_box], ccrs.PlateCarree(), facecolor='none',
edgecolor='blue', linewidth=1.0)
gl = ax.gridlines(crs=ccrs.PlateCarree(), draw_labels=True,
linewidth=0.2, color='gray', alpha=0.2, linestyle='-')
gl.top_labels = False
gl.left_labels = False
gl.xlines = False
gl.ylines = False
gl.xformatter = LONGITUDE_FORMATTER
gl.yformatter = LATITUDE_FORMATTER
#plt.savefig("/Users/robertocabieces/Documents/ISPshare/isp/mti/output/stations.png", bbox_inches='tight')
self.mpf.show()
