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Remove palettable #328

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merged 5 commits into from
Jun 13, 2020
Merged

Remove palettable #328

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00f0a2a
Removed palettable.
JS3xton May 6, 2020
e44e9c8
Change default colormap to emulate previous colormap.
JS3xton May 6, 2020
c02b5d0
Change default histogram colors for density_and_hist().
JS3xton May 9, 2020
e918053
Updated standard curve colors.
castillohair Jun 13, 2020
833a099
Changed standard curve color back to red.
castillohair Jun 13, 2020
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9 changes: 1 addition & 8 deletions FlowCal/mef.py
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Expand Up @@ -24,14 +24,7 @@
import FlowCal.transform
import FlowCal.stats

# Use default colors from palettable if available
try:
import palettable
except ImportError as e:
standard_curve_colors = ['b', 'g', 'r']
else:
standard_curve_colors = \
palettable.colorbrewer.qualitative.Paired_12.mpl_colors[1::2]
standard_curve_colors = ['tab:blue', 'tab:green', 'tab:red']

def clustering_gmm(data,
n_clusters,
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11 changes: 3 additions & 8 deletions FlowCal/plot.py
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Expand Up @@ -58,13 +58,7 @@
from matplotlib.font_manager import FontProperties
import warnings

# Use default colors from palettable if available
try:
import palettable
except ImportError as e:
cmap_default = plt.get_cmap(matplotlib.rcParams['image.cmap'])
else:
cmap_default = palettable.colorbrewer.diverging.Spectral_8_r.mpl_colormap
cmap_default = plt.get_cmap('Spectral_r')

savefig_dpi = 250

Expand Down Expand Up @@ -1786,7 +1780,8 @@ def density_and_hist(data,

# Colors
n_colors = n_plots - 1
colors = [cmap_default(i) for i in np.linspace(0, 1, n_colors)]
default_property_cycler = plt.rcParams['axes.prop_cycle']()
colors = [next(default_property_cycler)['color'] for i in range(n_colors)]
# Histogram
for i, hist_channel in enumerate(hist_channels):
# Define subplot
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3 changes: 1 addition & 2 deletions doc/getting_started/install_python.rst
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Expand Up @@ -14,7 +14,6 @@ Alternatively, download ``FlowCal`` from `here <https://github.com/taborlab/Flow
* ``numpy`` (>=1.8.2)
* ``scipy`` (>=0.14.0)
* ``matplotlib`` (>=2.0.0)
* ``palettable`` (>=2.1.1)
* ``scikit-image`` (>=0.10.0)
* ``scikit-learn`` (>=0.16.0)
* ``pandas`` (>=0.16.1)
Expand Down Expand Up @@ -52,4 +51,4 @@ Again, some users may need to precede the previous commands with ``sudo``.

sudo pip install --upgrade pip

After this, you may install ``FlowCal`` by following the steps above.
After this, you may install ``FlowCal`` by following the steps above.
1 change: 0 additions & 1 deletion requirements.txt
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Expand Up @@ -3,7 +3,6 @@ six>=1.10.0
numpy>=1.8.2
scipy>=0.14.0
matplotlib>=2.0.0
palettable>=2.1.1
scikit-image>=0.10.0
scikit-learn>=0.16.0
pandas>=0.16.1
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1 change: 0 additions & 1 deletion setup.py
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Expand Up @@ -90,7 +90,6 @@ def find_version(file_path):
'numpy>=1.8.2',
'scipy>=0.14.0',
'matplotlib>=2.0.0',
'palettable>=2.1.1',
'scikit-image>=0.10.0',
'scikit-learn>=0.16.0',
'pandas>=0.16.1',
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