Fc matplotlib

CHANGELOG.md

@@ -8,7 +8,7 @@
 
 ### fixed
 
-
+- matplotlib 3.9 issue with get_cmap ([API](https://matplotlib.org/stable/api/cm_api.html#:~:text=The%20colormap%20name%20can%20then%20be%20used%20as%20a%20string%20argument%20to%20any%20cmap%20parameter%20in%20Matplotlib.%20It%20is%20also%20available%20in%20pyplot.get_cmap.))
 
 ### dependencies
 

docs/release_notes.md

@@ -5,7 +5,21 @@
 
 ### added
 
+
+### fixed
+
+- matplotlib 3.9 issue with get_cmap ([API](https://matplotlib.org/stable/api/cm_api.html#:~:text=The%20colormap%20name%20can%20then%20be%20used%20as%20a%20string%20argument%20to%20any%20cmap%20parameter%20in%20Matplotlib.%20It%20is%20also%20available%20in%20pyplot.get_cmap.))
+
+### dependencies
+
+
+## v0.5.0
+
+### added
+
 - added Tangram to `deconvolution_spatial`
+- added scib metrics calculation to `integration`, using the [scib-metrics package](https://scib-metrics.readthedocs.io/en/latest/index.html)
+- [extra documentation](https://panpipes-pipelines.readthedocs.io/en/latest/)
 
 ### fixed
 

panpipes/funcs/plotting.py

@@ -3,7 +3,7 @@
 import matplotlib.pyplot as plt
 import seaborn as sns
 from scanpy.get import obs_df
-from matplotlib.cm import get_cmap
+from matplotlib.pyplot import get_cmap
 import itertools
 import logging
 from matplotlib import use

panpipes/python_scripts/plot_umaps_batch_correct.py

@@ -6,7 +6,7 @@
 import muon as mu
 import os
 import re
-from matplotlib import cm
+from matplotlib.pyplot import get_cmap
 from matplotlib.colors import ListedColormap
 import yaml 
 from panpipes.funcs.io import read_yaml
@@ -36,7 +36,7 @@
 L.info("Running with params: %s", args)
 palette_choice = ['#1f77b4', '#ff7f0e', '#2ca02c', '#d62728', '#9467bd', '#8c564b', '#e377c2', '#7f7f7f', '#bcbd22', '#17becf']
 # cmap_choice = "BuPu" # previous default = "viridis"
-bupu = cm.get_cmap('BuPu', 512)
+bupu = get_cmap('BuPu', 512)
 cmap_choice= ListedColormap(bupu(np.linspace(0.1, 1, 256)))
 dpi_use = 400 # previous default of 300 made the plots look blurry with high cell numbers (200k+)