fix: cci and interactive plot and type matplotlib

BiomedicalMachineLearning · Mar 8, 2023 · 10b105a · 10b105a
1 parent 89abaa9
commit 10b105a
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Showing 9 changed files with 40 additions and 33 deletions.
diff --git a/stlearn/plotting/cci_plot.py b/stlearn/plotting/cci_plot.py
@@ -434,7 +434,7 @@ def lr_result_plot(
     title: Optional["str"] = None,
     figsize: Optional[Tuple[float, float]] = None,
     cmap: Optional[str] = "Spectral_r",
-    ax: Optional[matplotlib.axes._subplots.Axes] = None,
+    ax: Optional[matplotlib.axes.Axes] = None,
     fig: Optional[matplotlib.figure.Figure] = None,
     show_plot: Optional[bool] = True,
     show_axis: Optional[bool] = False,
@@ -919,7 +919,7 @@ def het_plot(
     cmap: Optional[str] = "Spectral_r",
     use_label: Optional[str] = None,
     list_clusters: Optional[list] = None,
-    ax: Optional[matplotlib.axes._subplots.Axes] = None,
+    ax: Optional[matplotlib.axes.Axes] = None,
     fig: Optional[matplotlib.figure.Figure] = None,
     show_plot: Optional[bool] = True,
     show_axis: Optional[bool] = False,
@@ -1069,7 +1069,6 @@ def ccinet_plot(
 
     # Either plotting overall interactions, or just for a particular LR #
     int_df, title = get_int_df(adata, lr, use_label, sig_interactions, title)
-
     # Creating the interaction graph #
     all_set = int_df.index.values
     int_matrix = int_df.values

diff --git a/stlearn/plotting/cci_plot_helpers.py b/stlearn/plotting/cci_plot_helpers.py
@@ -417,19 +417,23 @@ def add_arrows_by_edges(
 def get_int_df(adata, lr, use_label, sig_interactions, title):
     """Retrieves the relevant interaction count matrix."""
     no_title = type(title) == type(None)
+    labels_ordered = adata.obs[use_label].cat.categories
     if type(lr) == type(None):  # No LR inputted, so just use all
         int_df = (
             adata.uns[f"lr_cci_{use_label}"]
             if sig_interactions
             else adata.uns[f"lr_cci_raw_{use_label}"]
-        )
+        )[labels_ordered].loc[labels_ordered]
         title = "Cell-Cell LR Interactions" if no_title else title
     else:
+
+        labels_ordered = adata.obs[use_label].cat.categories
         int_df = (
             adata.uns[f"per_lr_cci_{use_label}"][lr]
             if sig_interactions
             else adata.uns[f"per_lr_cci_raw_{use_label}"][lr]
-        )
+        )[labels_ordered].loc[labels_ordered]
+
         title = f"Cell-Cell {lr} interactions" if no_title else title
 
     return int_df, title

diff --git a/stlearn/plotting/classes.py b/stlearn/plotting/classes.py
@@ -41,7 +41,7 @@ def __init__(
         cmap: Optional[str] = "Spectral_r",
         use_label: Optional[str] = None,
         list_clusters: Optional[list] = None,
-        ax: Optional[matplotlib.axes._subplots.Axes] = None,
+        ax: Optional[matplotlib.axes.Axes] = None,
         fig: Optional[matplotlib.figure.Figure] = None,
         show_plot: Optional[bool] = True,
         show_axis: Optional[bool] = False,
@@ -244,7 +244,7 @@ def __init__(
         cmap: Optional[str] = "Spectral_r",
         use_label: Optional[str] = None,
         list_clusters: Optional[list] = None,
-        ax: Optional[matplotlib.axes._subplots.Axes] = None,
+        ax: Optional[matplotlib.axes.Axes] = None,
         fig: Optional[matplotlib.figure.Figure] = None,
         show_plot: Optional[bool] = True,
         show_axis: Optional[bool] = False,
@@ -457,7 +457,7 @@ def __init__(
         cmap: Optional[str] = "Spectral_r",
         use_label: Optional[str] = None,
         list_clusters: Optional[list] = None,
-        ax: Optional[matplotlib.axes._subplots.Axes] = None,
+        ax: Optional[matplotlib.axes.Axes] = None,
         fig: Optional[matplotlib.figure.Figure] = None,
         show_plot: Optional[bool] = True,
         show_axis: Optional[bool] = False,
@@ -627,7 +627,7 @@ def __init__(
         cmap: Optional[str] = "default",
         use_label: Optional[str] = None,
         list_clusters: Optional[list] = None,
-        ax: Optional[matplotlib.axes._subplots.Axes] = None,
+        ax: Optional[matplotlib.axes.Axes] = None,
         fig: Optional[matplotlib.figure.Figure] = None,
         show_plot: Optional[bool] = True,
         show_axis: Optional[bool] = False,
@@ -981,7 +981,7 @@ def __init__(
         cmap: Optional[str] = "jet",
         use_label: Optional[str] = None,
         list_clusters: Optional[list] = None,
-        ax: Optional[matplotlib.axes._subplots.Axes] = None,
+        ax: Optional[matplotlib.axes.Axes] = None,
         fig: Optional[matplotlib.figure.Figure] = None,
         show_plot: Optional[bool] = True,
         show_axis: Optional[bool] = False,
@@ -1135,7 +1135,7 @@ def __init__(
         cmap: Optional[str] = "Spectral_r",
         use_label: Optional[str] = None,
         list_clusters: Optional[list] = None,
-        ax: Optional[matplotlib.axes._subplots.Axes] = None,
+        ax: Optional[matplotlib.axes.Axes] = None,
         fig: Optional[matplotlib.figure.Figure] = None,
         show_plot: Optional[bool] = True,
         show_axis: Optional[bool] = False,
@@ -1205,7 +1205,7 @@ def __init__(
         figsize: Optional[Tuple[float, float]] = None,
         cmap: Optional[str] = "Spectral_r",
         list_clusters: Optional[list] = None,
-        ax: Optional[matplotlib.axes._subplots.Axes] = None,
+        ax: Optional[matplotlib.axes.Axes] = None,
         fig: Optional[matplotlib.figure.Figure] = None,
         show_plot: Optional[bool] = True,
         show_axis: Optional[bool] = False,

diff --git a/stlearn/plotting/classes_bokeh.py b/stlearn/plotting/classes_bokeh.py
@@ -75,7 +75,7 @@ def __init__(
         view = self.image.view(dtype=np.uint8).reshape((self.ydim, self.xdim, 4))
         # Copy the RGBA image into view, flipping it so it comes right-side up
         # with a lower-left origin
-        view[:, :, :] = np.flipud(np.asarray(img_pillow))
+        view[:, :, :] = np.asarray(img_pillow)
 
         # Display the 32-bit RGBA image
         self.dim = max(self.xdim, self.ydim)
@@ -159,7 +159,7 @@ def make_fig(self):
 
         fig = figure(
             title=self.gene_select.value,
-            x_range=(0, self.dim - 150),
+            x_range=(0, self.dim),
             y_range=(self.dim, 0),
             output_backend=self.output_backend.value,
             name="GenePlot",
@@ -173,7 +173,7 @@ def make_fig(self):
         fig.image_rgba(
             image=[self.image],
             x=0,
-            y=self.xdim,
+            y=0,
             dw=self.ydim,
             dh=self.xdim,
             global_alpha=self.tissue_alpha.value,
@@ -251,11 +251,11 @@ def add_violin(self):
         view2 = image2.view(dtype=np.uint8).reshape((ydim, xdim, 4))
         # Copy the RGBA image into view, flipping it so it comes right-side up
         # with a lower-left origin
-        view2[:, :, :] = np.flipud(np.asarray(img_pillow2))
+        view2[:, :, :] = np.asarray(img_pillow2)
 
         p = figure(
-            plot_width=910,
-            plot_height=int(910 / xdim * ydim) + 5,
+            width=910,
+            height=int(910 / xdim * ydim) + 5,
             output_backend=self.output_backend.value,
         )
 
@@ -346,7 +346,7 @@ def __init__(
         view = self.image.view(dtype=np.uint8).reshape((self.ydim, self.xdim, 4))
         # Copy the RGBA image into view, flipping it so it comes right-side up
         # with a lower-left origin
-        view[:, :, :] = np.flipud(np.asarray(img_pillow))
+        view[:, :, :] = np.asarray(img_pillow)
 
         # Display the 32-bit RGBA image
         self.dim = max(self.xdim, self.ydim)
@@ -556,7 +556,7 @@ def make_fig(self):
         fig.image_rgba(
             image=[self.image],
             x=0,
-            y=self.xdim,
+            y=0,
             dw=self.ydim,
             dh=self.xdim,
             global_alpha=self.tissue_alpha.value,
@@ -682,11 +682,11 @@ def add_dea(self):
         view2 = image2.view(dtype=np.uint8).reshape((ydim, xdim, 4))
         # Copy the RGBA image into view, flipping it so it comes right-side up
         # with a lower-left origin
-        view2[:, :, :] = np.flipud(np.asarray(img_pillow2))
+        view2[:, :, :] = np.asarray(img_pillow2)
 
         p = figure(
-            plot_width=910,
-            plot_height=int(910 / xdim * ydim) + 5,
+            width=910,
+            height=int(910 / xdim * ydim) + 5,
             output_backend=self.output_backend.value,
         )
 
@@ -796,7 +796,7 @@ def __init__(
         view = self.image.view(dtype=np.uint8).reshape((self.ydim, self.xdim, 4))
         # Copy the RGBA image into view, flipping it so it comes right-side up
         # with a lower-left origin
-        view[:, :, :] = np.flipud(np.asarray(img_pillow))
+        view[:, :, :] = np.asarray(img_pillow)
 
         # Display the 32-bit RGBA image
         self.dim = max(self.xdim, self.ydim)
@@ -883,7 +883,7 @@ def make_fig(self):
         fig.image_rgba(
             image=[self.image],
             x=0,
-            y=self.xdim,
+            y=0,
             dw=self.ydim,
             dh=self.xdim,
             global_alpha=self.tissue_alpha.value,
@@ -975,7 +975,7 @@ def __init__(
         view = self.image.view(dtype=np.uint8).reshape((self.ydim, self.xdim, 4))
         # Copy the RGBA image into view, flipping it so it comes right-side up
         # with a lower-left origin
-        view[:, :, :] = np.flipud(np.asarray(img_pillow))
+        view[:, :, :] = np.asarray(img_pillow)
 
         # Display the 32-bit RGBA image
         self.dim = max(self.xdim, self.ydim)
@@ -1072,7 +1072,7 @@ def make_fig(self):
         fig.image_rgba(
             image=[self.image],
             x=0,
-            y=self.xdim,
+            y=0,
             dw=self.ydim,
             dh=self.xdim,
             global_alpha=self.tissue_alpha.value,
@@ -1264,7 +1264,7 @@ def __init__(
         view = self.image.view(dtype=np.uint8).reshape((self.ydim, self.xdim, 4))
         # Copy the RGBA image into view, flipping it so it comes right-side up
         # with a lower-left origin
-        view[:, :, :] = np.flipud(np.asarray(img_pillow))
+        view[:, :, :] = np.asarray(img_pillow)
 
         # Display the 32-bit RGBA image
         self.dim = max(self.xdim, self.ydim)
@@ -1320,7 +1320,7 @@ def make_fig(self):
         fig.image_rgba(
             image=[self.image],
             x=0,
-            y=self.xdim,
+            y=0,
             dw=self.ydim,
             dh=self.xdim,
             global_alpha=self.tissue_alpha.value,

diff --git a/stlearn/plotting/cluster_plot.py b/stlearn/plotting/cluster_plot.py
@@ -30,7 +30,7 @@ def cluster_plot(
     cmap: Optional[str] = "default",
     use_label: Optional[str] = None,
     list_clusters: Optional[list] = None,
-    ax: Optional[matplotlib.axes._subplots.Axes] = None,
+    ax: Optional[matplotlib.axes.Axes] = None,
     fig: Optional[matplotlib.figure.Figure] = None,
     show_plot: Optional[bool] = True,
     show_axis: Optional[bool] = False,

diff --git a/stlearn/plotting/feat_plot.py b/stlearn/plotting/feat_plot.py
@@ -35,7 +35,7 @@ def feat_plot(
     cmap: Optional[str] = "Spectral_r",
     use_label: Optional[str] = None,
     list_clusters: Optional[list] = None,
-    ax: Optional[matplotlib.axes._subplots.Axes] = None,
+    ax: Optional[matplotlib.axes.Axes] = None,
     fig: Optional[matplotlib.figure.Figure] = None,
     show_plot: Optional[bool] = True,
     show_axis: Optional[bool] = False,

diff --git a/stlearn/plotting/gene_plot.py b/stlearn/plotting/gene_plot.py
@@ -33,7 +33,7 @@ def gene_plot(
     cmap: Optional[str] = "Spectral_r",
     use_label: Optional[str] = None,
     list_clusters: Optional[list] = None,
-    ax: Optional[matplotlib.axes._subplots.Axes] = None,
+    ax: Optional[matplotlib.axes.Axes] = None,
     fig: Optional[matplotlib.figure.Figure] = None,
     show_plot: Optional[bool] = True,
     show_axis: Optional[bool] = False,

diff --git a/stlearn/utils.py b/stlearn/utils.py
@@ -26,7 +26,7 @@ class Empty(Enum):
 from abc import ABC
 
 
-class _AxesSubplot(Axes, axes.SubplotBase, ABC):
+class _AxesSubplot(Axes, axes.SubplotBase):
     """Intersection between Axes and SubplotBase: Has methods of both"""
 
 

diff --git a/stlearn/wrapper/read.py b/stlearn/wrapper/read.py
@@ -193,6 +193,10 @@ def Read10X(
     adata.obs["imagerow"] = image_coor[:, 1]
     adata.uns["spatial"][library_id]["use_quality"] = quality
 
+    adata.obs["array_row"] = adata.obs["array_row"].astype(int)
+    adata.obs["array_col"] = adata.obs["array_col"].astype(int)
+    adata.obsm["spatial"] = adata.obsm["spatial"].astype("int64")
+
     return adata