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better alluvial diagrams; better docs
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@j-i-l
j-i-l committed Feb 20, 2020
1 parent 6bf3625 commit 66e3587
Showing 1 changed file with 153 additions and 84 deletions.
237 changes: 153 additions & 84 deletions majortrack/tracker.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2150,30 +2150,61 @@ def get_alluvialdiagram(
If `iterator is not provided, then the alluvialdiagram will contain all
the clustrings in the time series.
Parameters:
-----------
:param kwargs:
options:
--------
- cluster_location: 'center', 'start, 'end' location withing the
aggregation time window where the cluster should be put.
Default is 'center'
- cluster_width: with of the clusters
- cluster_label: None (default), 'groupsize', 'group_index'
- merged_edgecolor: edgecolor of merged groups
- merged_facecolor: facecolor of merged groups
- merged_linewidth: linewidth of merged groups
- cluster_facecolor: either single color or dict with idx as keys
holding a dict with group_id as key
- cluster_edgecolor: either single color or dict with idx as keys
holding a dict with group_id as key
- flux_facecolor: either single color or dict with idx as keys
holding a dict with cluster tuple as key, with the first
element a group id form time step idx and the second a group id
form time step idx+1
- new_coloring: False
- distinct_colors: can be an instance of DistinctColors that will
be used for the coloring
Parameters
==========
axes: :obj:`matplotlib.axes.Axes`
Axes to draw an Alluvial diagram on.
iterator: iter (default=None)
An iterator for the indices of the time series to include in the
alluvial diagram. If not provided then the entire time series is
used.
cluster_width: float
with of the clusters. This should be provided in the same units as
:attr:`~Majortrack.timepoints`.
\*args optional parameter:
Will be forwarded to the :class:`pyalluv.AlluvialPlot` call.
\**kwargs optional parameter:
cluster_location: str (default='center')
either 'center', 'start, 'end' location withing the aggregation
time window where the cluster should be put.
cluster_label: str (default=None)
determine how to label cluster. Possible options are:
* 'groupsize'
* 'group_index'
merged_edgecolor: str (default=None)
edgecolor of merged clusters.
merged_facecolor: str (default=None)
facecolor of merged clusters.
merged_linewidth: float (default=None)
linewidth of merged clusters.
cluster_facecolor: str, dict(dict)
facecolor of clusters. Either provide a single color or a `dict`
with indices of the time series as keys, holding a dict with
cluster_id as key and colours as values.
cluster_edgecolor: str, dict(dict)
edgecolor of clusters. Either provide a single color or a `dict`
with indices of the time series as keys, holding a dict with
cluster_id as key and colours as values.
flux_facecolor: str, dict
either provide a single color, a keyword or a dict.
Valid keywords are: ``'cluster'``.
If a dictionary is provided then the `idx` of the time series must
be the keys with another dict as value holding a dict with a tuple
as key and a color as value. The tuple's first element must be a
group id form time step `idx` and the second a group id k form time
step `idx`+1
new_coloring: bool (default=False)
if a new color sequence should be generated or not.
distinct_colors: :obj:`colorseq.DistinctColors` (default=None)
the sequence of distinct colour to use.
target_clusters: list (default=None)
list of dynamic cluster id's to display in the alluvial diagram.
If provided, only the dynamic clusters specified in this list
will be displayed.
"""
assert self.clusterings is not None
# from matplotlib import pyplot as plt
Expand Down Expand Up @@ -2330,6 +2361,35 @@ def _get_cluster_edgecolor(idx, group_id): return _dnec
else:
_get_flux_linewidth = _def_linewidth

target_clusters = kwargs.get('target_clusters', False)
if not target_clusters:
def include_cluster(idx, group):
return True
else:
def include_cluster(idx, group):
if any(
[
indiv in self.comm_members[idx][comm]
for indiv in group
for comm in target_clusters
if comm in self.comm_members[idx]
]
):
return True
elif idx and any(
[
indiv in self.comm_members[idx-1][comm]
for indiv in group
for comm in target_clusters
if comm in self.comm_members[idx-1]
]
):
# check if in the previous snapshot members of this group
# were in the target_clusters
return True
else:
return False

merged_edgecolor = kwargs.get('merged_edgecolor', None)
merged_facecolor = kwargs.get('merged_facecolor', None)
merged_linewidth = kwargs.get('merged_linewidth', None)
Expand Down Expand Up @@ -2362,44 +2422,47 @@ def _get_cluster_edgecolor(idx, group_id): return _dnec
tp_clusters = []
for _i in range(len(_grouping)):
_group = _grouping[_i]
# is it a merged group
_facecolor = _get_cluster_facecolor(idx, _i)
_edgecolor = _get_cluster_edgecolor(idx, _i)
_linewidth = _get_cluster_linewidth(idx, _i)
if isinstance(cluster_label_margin, dict):
_label_margin = cluster_label_margin[idx][_i]
elif isinstance(cluster_label_margin, (tuple, list)):
_label_margin = cluster_label_margin
else:
_label_margin = (0.4 * cluster_width, 0.1)
if _edgecolor is None:
_edgecolor = _facecolor
if treat_mergeds:
if idx < len(self.cluster_trace):
if self.cluster_trace[idx][_i] < 0:
if merged_linewidth is not None:
_linewidth = merged_linewidth
if merged_edgecolor is not None:
_edgecolor = merged_edgecolor
if merged_facecolor is not None:
_facecolor = merged_facecolor
if cluster_label == 'groupsize':
c_label = '{0}'.format(len(_group))
elif cluster_label == 'group_index':
c_label = '{0}'.format(_i)
else:
c_label = None
tp_clusters.append(
Cluster(
height=len(_group),
width=cluster_width,
facecolor=_facecolor,
edgecolor=_edgecolor,
lw=_linewidth,
label=c_label,
label_margin=_label_margin
if include_cluster(idx, _group):
# is it a merged group
_facecolor = _get_cluster_facecolor(idx, _i)
_edgecolor = _get_cluster_edgecolor(idx, _i)
_linewidth = _get_cluster_linewidth(idx, _i)
if isinstance(cluster_label_margin, dict):
_label_margin = cluster_label_margin[idx][_i]
elif isinstance(cluster_label_margin, (tuple, list)):
_label_margin = cluster_label_margin
else:
_label_margin = (0.4 * cluster_width, 0.1)
if _edgecolor is None:
_edgecolor = _facecolor
if treat_mergeds:
if idx < len(self.cluster_trace):
if self.cluster_trace[idx][_i] < 0:
if merged_linewidth is not None:
_linewidth = merged_linewidth
if merged_edgecolor is not None:
_edgecolor = merged_edgecolor
if merged_facecolor is not None:
_facecolor = merged_facecolor
if cluster_label == 'groupsize':
c_label = '{0}'.format(len(_group))
elif cluster_label == 'group_index':
c_label = '{0}'.format(_i)
else:
c_label = None
tp_clusters.append(
Cluster(
height=len(_group),
width=cluster_width,
facecolor=_facecolor,
edgecolor=_edgecolor,
lw=_linewidth,
label=c_label,
label_margin=_label_margin
)
)
)
else:
tp_clusters.append(None)
_clusters.append(tp_clusters)
# 2nd round to set the fluxes
if iterator is None:
Expand All @@ -2412,30 +2475,36 @@ def _get_cluster_edgecolor(idx, group_id): return _dnec
_prev_grouping = self.clusterings[prev_idx]
_x_pos_fluxes = []
for _i in range(len(_grouping)):
for _j in range(len(_prev_grouping)):
_intersect = len(
_prev_grouping[_j].intersection(
_grouping[_i]
)
)
_linewidth = _get_flux_linewidth(prev_idx, _j, _i)
if _intersect:
_facecolor = _get_flux_facecolor(prev_idx, _j, _i)
_edgecolor = _get_flux_edgecolor(prev_idx, _j, _i)
if _edgecolor is None:
_edgecolor = _facecolor
_x_pos_fluxes.append(
[
Flux(
flux=_intersect,
source_cluster=_clusters[prev_idx][_j],
target_cluster=_clusters[idx][_i],
facecolor=_facecolor,
edgecolor=_edgecolor,
lw=_linewidth
if include_cluster(idx, _grouping[_i]):
for _j in range(len(_prev_grouping)):
if include_cluster(idx-1, _prev_grouping[_j]):
_intersect = len(
_prev_grouping[_j].intersection(
_grouping[_i]
)
)
_linewidth = _get_flux_linewidth(prev_idx, _j, _i)
if _intersect:
_facecolor = _get_flux_facecolor(
prev_idx, _j, _i)
_edgecolor = _get_flux_edgecolor(
prev_idx, _j, _i)
if _edgecolor is None:
_edgecolor = _facecolor
_x_pos_fluxes.append(
[
Flux(
flux=_intersect,
source_cluster=_clusters[
prev_idx][_j],
target_cluster=_clusters[
idx][_i],
facecolor=_facecolor,
edgecolor=_edgecolor,
lw=_linewidth
)
]
)
]
)
_fluxes.append(
_x_pos_fluxes
)
Expand Down

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