diff --git a/ariaec/econverter.pyc b/ariaec/econverter.pyc
index 81fa84027c6739ce54a70a6ad347b328da8c30a4..e3481cf613ef97b7a6d67d480cabccf0baa8baa9 100644
Binary files a/ariaec/econverter.pyc and b/ariaec/econverter.pyc differ
diff --git a/ariaec/ecsettings.pyc b/ariaec/ecsettings.pyc
index 19f73a296b5c13e0ec0d16e4b6f932549dfd827b..b44fb90f2a6510c1985e58448fbbea72f8fd679c 100644
Binary files a/ariaec/ecsettings.pyc and b/ariaec/ecsettings.pyc differ
diff --git a/ariaec/maplot.py b/ariaec/maplot.py
index f5800cf9f92f6773b9475d2acddeca0ef7f34b59..2be61d14ded7358034d234cc43a882f70412052f 100644
--- a/ariaec/maplot.py
+++ b/ariaec/maplot.py
@@ -72,17 +72,25 @@ class AriaEcContactMap(object):
nb_c = int(len(self.protein.aa_sequence.sequence) *
self.settings.setup.config.get("n_factor"))
+ refmap = self.refmap["contactmap"]
+ plotparams = {k: self.settings.contactmap.config.get(k, None)
+ for k in ('size_fig', 'plot_ext', 'plot_dpi')}
for mapt in self.allresmap.keys():
+ outdir = self.settings.outdir
+ prefix = "_".join((self.outprefix, mapt, self.reftype))
if mapt == self.reftype:
+ refmap.write_contacts("_".join((self.outprefix, mapt)),
+ outdir=outdir)
+ refmap.saveplot(outdir=outdir,
+ outprefix="_".join((self.outprefix, mapt)),
+ **plotparams)
continue
- refmap = self.refmap["contactmap"]
if self.allresmap[mapt].get("contactmap") is not None and \
self.allresmap[mapt].get("scoremap") is not None:
- prefix = "_".join((self.outprefix, mapt, self.reftype))
- outdir = self.settings.outdir
if not self.settings.contactmap.args.get("nofilter"):
+ # Get filtered contact map/list
cmpmap = self.allresmap[mapt]["contactmap"].topmap(
self.allresmap[mapt]["scoremap"], nb_c)
cmplist = self.allresmap[mapt]['scoremap'].sortedset(
@@ -101,9 +109,11 @@ class AriaEcContactMap(object):
# TODO: elementwise error with compare method
refmap.compare(cmpmap, outprefix=prefix,
out_dir=outdir,
- **{k: self.settings.contactmap.config.get(k, None)
- for k in ('save_fig', 'size_fig',
- 'plot_ext', 'plot_dpi', 'alpha')})
+ save_fig=self.settings.contactmap.config.get(
+ "save_fig"),
+ alpha=self.settings.contactmap.config.get(
+ "alpha"),
+ **plotparams)
logger.info(pd.crosstab(cmpmap.to_series(), refmap.to_series(),
rownames=[mapt],
colnames=[self.reftype]))
@@ -123,9 +133,11 @@ class AriaEcContactMap(object):
# TODO: elementwise error with compare method
refmap.compare(cmpmap, outprefix=prefix,
out_dir=outdir,
- **{k: self.settings.contactmap.config.get(k, None)
- for k in ('save_fig', 'size_fig',
- 'plot_ext', 'plot_dpi', 'alpha')})
+ save_fig=self.settings.contactmap.config.get(
+ "save_fig"),
+ alpha=self.settings.contactmap.config.get(
+ "alpha"),
+ **plotparams)
logger.info(pd.crosstab(cmpmap.to_series(), refmap.to_series(),
rownames=[mapt], colnames=[self.reftype]))
else:
diff --git a/ariaec/maplot.pyc b/ariaec/maplot.pyc
index 8fd4173edea62cd64849117317a17db95abb7157..9309021709176257fae3c5271192e2a9f44936cd 100644
Binary files a/ariaec/maplot.pyc and b/ariaec/maplot.pyc differ
diff --git a/ariaec/protein.pyc b/ariaec/protein.pyc
index 403f62a32dae04748fa0616abf20cdc067c654cc..5d811cfb9d7a9306750c04658f30e0269554a469 100644
Binary files a/ariaec/protein.pyc and b/ariaec/protein.pyc differ
diff --git a/ariaec/protmap.py b/ariaec/protmap.py
index 719dad83cd8a9fbfe9ee9f24891dfe219e18b12a..d5c475286c36d3885d5a5eab9523244e4711bc0e 100644
--- a/ariaec/protmap.py
+++ b/ariaec/protmap.py
@@ -168,6 +168,7 @@ class ProteinMap(Map):
kwargs["columns"] = col
super(ProteinMap, self).__init__(**kwargs)
self.contact_flags = flaglist if flaglist else None
+ self._maplot = None
def _constructor_expanddim(self):
super(ProteinMap, self)._constructor_expanddim()
@@ -176,6 +177,34 @@ class ProteinMap(Map):
def sequence(self):
raise NotImplementedError
+ @property
+ def maplot(self):
+ # Contact map Plot
+ if not self._maplot:
+ minticks = tickmin(self, shift=1) # Nb graduations
+
+ self._maplot = sns.heatmap(self, square=True, cbar=False,
+ linewidths=1, vmax=1, vmin=-1,
+ cmap=sns.diverging_palette(20, 220, n=7,
+ as_cmap=True),
+ xticklabels=minticks[0],
+ yticklabels=minticks[1])
+ return self._maplot
+
+ def saveplot(self, outdir='', outprefix="protein", size_fig=10,
+ plot_ext="pdf", plot_dpi=200):
+ f, ax = plt.subplots(figsize=(12, 9))
+ tickrot(self.maplot.axes, self.maplot.figure,
+ rotype='horizontal')
+ self.maplot.figure.set_size_inches(size_fig, size_fig)
+ map_title = "%s contacts map" % outprefix
+ self.maplot.set_title(map_title)
+ self.maplot.figure.tight_layout()
+
+ f.tight_layout()
+ self.maplot.figure.savefig(os.path.join(outdir, "%s.contactmap.%s" % (
+ outprefix, plot_ext)), dpi=plot_dpi)
+
def contactset(self, human_idx=False):
# Remove duplicate in contact_list
if self.contact_list():
@@ -215,8 +244,7 @@ class ProteinMap(Map):
# Indexation matrice (tous les atomes ou tous les residus)
raise NotImplementedError
- def compare(self, protmap, save_fig=True, out_dir='', outprefix="protein",
- size_fig=10, plot_ext="pdf", plot_dpi=200, alpha=None):
+ def compare(self, protmap, save_fig=True, alpha=None, **kwargs):
# Contact map plot
if getattr(protmap, "shape") and self.shape != protmap.shape:
logging.error("Cant't compare %s map with %s" % (
@@ -224,14 +252,14 @@ class ProteinMap(Map):
return None
else:
# Contact map Plot
- minticks = tickmin(self, shift=1) # Nb graduations
- f, ax = plt.subplots(figsize=(12, 9))
- contactmaplot = sns.heatmap(self, square=True, cbar=False,
- linewidths=1, vmax=1, vmin=-1,
- cmap=sns.diverging_palette(20, 220, n=7,
- as_cmap=True),
- xticklabels=minticks[0],
- yticklabels=minticks[1])
+ # minticks = tickmin(self, shift=1) # Nb graduations
+ # f, ax = plt.subplots(figsize=(12, 9))
+ # contactmaplot = sns.heatmap(self, square=True, cbar=False,
+ # linewidths=1, vmax=1, vmin=-1,
+ # cmap=sns.diverging_palette(20, 220, n=7,
+ # as_cmap=True),
+ # xticklabels=minticks[0],
+ # yticklabels=minticks[1])
cmplist = protmap.contact_list()
ymax = len(self.sequence) - 1
@@ -250,9 +278,9 @@ class ProteinMap(Map):
color = pal[i]
mark = Line2D.filled_markers[i]
for x, y in zip(xind, yind):
- contactmaplot.axes.scatter(x, y, s=20, c=color,
- linewidths=0,
- alpha=alpha, marker=mark)
+ self.maplot.axes.scatter(x, y, s=20, c=color,
+ linewidths=0, alpha=alpha,
+ marker=mark)
else:
xind = [x + .5 for x in
zip(*cmplist)[0] + zip(*cmplist)[1]]
@@ -262,27 +290,24 @@ class ProteinMap(Map):
# width = [0.3 for _ in xind]
# for x, y, h in zip(xind, yind, width):
for x, y in zip(xind, yind):
- contactmaplot.axes.scatter(x, y, s=20, c=color,
- linewidths=0,
- alpha=alpha)
- # contactmaplot.axes.add_artist(ptc.Circle(xy=(x, y), alpha=alpha,
- # color="green",
- # radius=h))
+ self.maplot.axes.scatter(x, y, s=20, c=color, linewidths=0,
+ alpha=alpha)
if save_fig:
- tickrot(contactmaplot.axes, contactmaplot.figure,
- rotype='horizontal')
- contactmaplot.figure.set_size_inches(size_fig,
- size_fig)
- map_title = "%s contacts map" % outprefix
- contactmaplot.set_title(map_title)
- contactmaplot.figure.tight_layout()
-
- f.tight_layout()
- contactmaplot.figure.savefig(os.path.join(out_dir,
- "%s.contactmap.%s" % (
- outprefix,
- plot_ext)),
- dpi=plot_dpi)
+ self.saveplot(**kwargs)
+ # tickrot(contactmaplot.axes, contactmaplot.figure,
+ # rotype='horizontal')
+ # contactmaplot.figure.set_size_inches(size_fig,
+ # size_fig)
+ # map_title = "%s contacts map" % outprefix
+ # contactmaplot.set_title(map_title)
+ # contactmaplot.figure.tight_layout()
+ #
+ # f.tight_layout()
+ # contactmaplot.figure.savefig(os.path.join(out_dir,
+ # "%s.contactmap.%s" % (
+ # outprefix,
+ # plot_ext)),
+ # dpi=plot_dpi)
def compare_contactmap(self, cmpmap, contactlist, outprefix, outdir="",
distmap=None,
@@ -438,6 +463,7 @@ class ResAtmMap(ProteinMap):
if self.dtype == bool:
# If self is already a contact map
return None
+ # TODO: issue with sc_sc treshold !!!!!
logger.info("Generate contact map using contact definition %s" %
contactdef)
# Contact map initialize to a boolean matrix filled with False
@@ -457,12 +483,14 @@ class ResAtmMap(ProteinMap):
atm_list = set(self.index.get_level_values(1))
atms_list = set([(a, b) for a in atm_list for b in atm_list])
for pair in contactdef.keys():
+ if pair == "default_cutoff":
+ continue
treshold = contactdef[pair]
pair = tuple(pair.upper().split("_"))
- if pair not in atms_list:
- # Already applied a treshold for this pair
- continue
- elif pair == ("SC", "SC"):
+ logger.info(
+ "Filtering values in matrix related to %s (%s)" %
+ (str(pair), str(treshold)))
+ if pair in (("SC", "SC"), ("sc", "sc")):
# Use scsc_min to apply treshold only for selected atom
# sidechain
idx_list = []
@@ -480,13 +508,14 @@ class ResAtmMap(ProteinMap):
pair[1]) and x[1] == atm2))
mask = ([any(tup) for tup in zip(*idx_list)],
[any(tup) for tup in zip(*col_list)])
+ elif pair not in atms_list:
+ logger.error("Pair %s doesn't exist ..." % str(pair))
+ # Already applied a treshold for this pair
+ continue
else:
logger.debug("Apply treshold for %s" % str(pair))
atms_list.discard(pair)
# Selecting rows for each atom
- logger.info(
- "Filtering values in matrix related to %s (%s)" %
- (str(pair), str(treshold)))
mask = (self.index.get_level_values(1) == pair[0],
self.index.get_level_values(1) == pair[1])
tmp = self.loc[mask].apply(lambda x: x < float(treshold))
@@ -946,7 +975,7 @@ class MapFilter:
if mapfilters == "all":
mapfilters = self.filter_types
elif not mapfilters:
- mapfilters = ["pos", ]
+ mapfilters = ["pos"]
else:
if type(mapfilters) == list:
mapfilters = [elm for elm in mapfilters if elm in self.filter_types]
diff --git a/ariaec/protmap.pyc b/ariaec/protmap.pyc
index 8183bad2755bd1f3ffeb4920ab8b9412ecfc17e4..a7d3811e93dd82a249644f868314f5b3e3353fe5 100644
Binary files a/ariaec/protmap.pyc and b/ariaec/protmap.pyc differ
diff --git a/ariaec/reader.pyc b/ariaec/reader.pyc
index 3a3e015d302ea5a636aa5ec9cbe225a0659cbaea..5eeb4d61ab4ba9568ce24f11b49683d31a4434f0 100644
Binary files a/ariaec/reader.pyc and b/ariaec/reader.pyc differ