small bugs

labsyspharm · Mar 18, 2024 · 90ed47f · 90ed47f
1 parent 2ce9bf7
commit 90ed47f
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Showing 7 changed files with 898 additions and 26 deletions.
diff --git a/docs/tutorials/nbs/Prior knowledge based phenotyping.ipynb b/docs/tutorials/nbs/Prior knowledge based phenotyping.ipynb
diff --git a/docs/tutorials/nbs/Unsupervised clustering to phenotype cells.ipynb b/docs/tutorials/nbs/Unsupervised clustering to phenotype cells.ipynb
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,7 +1,7 @@
 [tool.poetry]
 
 name = "SCIMAP"
-version = "1.3.9"
+version = "1.3.10"
 description = "Spatial Single-Cell Analysis Toolkit"
 
 license = "MIT"

diff --git a/scimap/plotting/groupCorrelation.py b/scimap/plotting/groupCorrelation.py
@@ -21,6 +21,13 @@
 from scipy.stats import zscore
 import argparse
 
+
+plt.rcParams['figure.dpi'] = 100
+plt.rcParams['savefig.dpi']=300
+plt.rcParams['font.family']='sans serif'
+plt.rcParams['font.sans-serif']='Arial'
+plt.rcParams['pdf.fonttype']=42
+
 # function
 def groupCorrelation(adata, 
                      groupBy, 

diff --git a/scimap/plotting/heatmap.py b/scimap/plotting/heatmap.py
@@ -24,6 +24,13 @@
 import argparse
 
 
+plt.rcParams['figure.dpi'] = 100
+plt.rcParams['savefig.dpi']=300
+plt.rcParams['font.family']='sans serif'
+plt.rcParams['font.sans-serif']='Arial'
+plt.rcParams['pdf.fonttype']=42
+
+
 # function
 def heatmap (adata,
              groupBy,
@@ -299,7 +306,6 @@ def plot_category_heatmap_vectorized(data,
         cbar_ax.xaxis.set_label_position('top')
         cbar.set_label('Mean expression in group')
 
-        ax.set_title('Heatmap of Marker Values by Category')
         ax.set_xlabel('Markers')
         ax.set_ylabel('Categories')
 

diff --git a/scimap/plotting/markerCorrelation.py b/scimap/plotting/markerCorrelation.py
@@ -21,6 +21,13 @@
 import warnings
 import argparse
 
+
+plt.rcParams['figure.dpi'] = 100
+plt.rcParams['savefig.dpi']=300
+plt.rcParams['font.family']='sans serif'
+plt.rcParams['font.sans-serif']='Arial'
+plt.rcParams['pdf.fonttype']=42
+
 def markerCorrelation (adata, 
                        layer='log', 
                        subsetMarkers=None, 

diff --git a/scimap/plotting/umap.py b/scimap/plotting/umap.py
@@ -29,13 +29,16 @@
 import seaborn as sns
 import matplotlib.patches as mpatches
 
-import matplotlib as mpl
-mpl.rcParams['pdf.fonttype'] = 42
+plt.rcParams['figure.dpi'] = 100
+plt.rcParams['savefig.dpi']=300
+plt.rcParams['font.family']='sans serif'
+plt.rcParams['font.sans-serif']='Arial'
+plt.rcParams['pdf.fonttype']=42
 
 # function
 def umap (adata, 
           color=None, 
-          use_layer=None, 
+          layer=None, 
           use_raw=False, 
           log=False, 
           label='umap',
@@ -57,7 +60,7 @@ def umap (adata,
             List of keys from `adata.obs.columns` or `adata.var.index` to color the plot. 
             Allows multiple keys for facetted plotting.
 
-        use_layer (str, optional):  
+        layer (str, optional):  
             Specifies the AnnData layer to use for UMAP calculations. Defaults to using `adata.X`.
 
         use_raw (bool, optional):  
@@ -138,14 +141,16 @@ def umap (adata,
         # organise the data
         if any(item in color for item in list(adata.obs.columns)):
             adataobs = adata.obs.loc[:, adata.obs.columns.isin(color)]
+            adataobs = adataobs.apply(lambda x: x.astype('category'))
+
         else:
             adataobs = None
 
         if any(item in color for item in list(adata.var.index)):
             # find the index of the marker
             marker_index = np.where(np.isin(list(adata.var.index), color))[0]
-            if use_layer is not None:
-                adatavar = adata.layers[use_layer][:, np.r_[marker_index]]
+            if layer is not None:
+                adatavar = adata.layers[layer][:, np.r_[marker_index]]
             elif use_raw is True:
                 adatavar = adata.raw.X[:, np.r_[marker_index]]
             else: