Fix label plot

Signed-off-by: zethson <[email protected]>

CHANGELOG.md

@@ -10,7 +10,7 @@
 ### fixed
 
 - fixed error in `vis`
-    - error occurred when only wanting to plot continuous or categorical variables (or neither), not both 
+    - error occurred when only wanting to plot continuous or categorical variables (or neither), not both
 
 ### dependencies
 

README.md

@@ -4,7 +4,7 @@
 
 ## Overview
 
-Panpipes is a set of computational workflows designed to automate multimodal single-cell and spatial transcriptomic analyses by incorporating widely-used Python-based tools to perform quality control, preprocessing, integration, clustering, and reference mapping at scale. 
+Panpipes is a set of computational workflows designed to automate multimodal single-cell and spatial transcriptomic analyses by incorporating widely-used Python-based tools to perform quality control, preprocessing, integration, clustering, and reference mapping at scale.
 Panpipes allows reliable and customisable analysis and evaluation of individual and integrated modalities, thereby empowering decision-making before downstream investigations.
 
 **See our [documentation](https://panpipes-pipelines.readthedocs.io/en/latest/) and our [preprint](https://www.biorxiv.org/content/10.1101/2023.03.11.532085v2)**  
@@ -45,4 +45,4 @@ bioRxiv 2023.03.11.532085; doi: https://doi.org/10.1101/2023.03.11.532085](https
 ## Contributors
 
 Created and Maintained by Charlotte Rich-Griffin and Fabiola Curion.
-Additional contributors: Sarah Ouologuem, Devika Agarwal, Lilly May, Kevin Rue-Albrecht.
+Additional contributors: Sarah Ouologuem, Devika Agarwal, Lilly May, Kevin Rue-Albrecht, Lukas Heumos.

panpipes/funcs/plotting.py

@@ -313,7 +313,7 @@ def ridgeplot(adata, features, layer=None, splitplot=3, bandwidth=0.1):
         for tick in ax.get_yticklabels():
             tick.set_fontsize(10)
         for tick in ax.yaxis.get_major_ticks():
-            tick.label.set_verticalalignment("bottom")
+            tick.label1.set_verticalalignment("bottom")
 
     fig.tight_layout()
     return fig, ax

panpipes/python_scripts/run_preprocess_prot.py

@@ -67,9 +67,6 @@
 
 
 args, opt = parser.parse_known_args()
-# args = argparse.Namespace(filtered_mudata='test.h5mu', 
-# bg_mudata='/well/cartography/users/zsj686/non_cart_projects/005-multimodal_scpipelines/ingest/test_raw.h5mu', 
-# channel_col=None, normalisation_methods='clr,dsb', clr_margin='0', quantile_clipping='True', figpath='./figures/prot', save_mtx=False, save_mudata_path='test.h5mu')
 save_mtx=pnp.pp.check_for_bool(args.save_mtx)
 
 norm_methods = args.normalisation_methods.split(',')
@@ -85,9 +82,7 @@
 sc.set_figure_params(scanpy=True, fontsize=14, dpi=300, facecolor='white', figsize=(5,5))
 
 
-
 # load filtered data - if use_muon is True this will return a mudata object, else returns an mudata object
-
 L.info("reading filtered mudata object")
 try:
     all_mdata = mu.read(args.filtered_mudata)