Error when running st.pl.cluster_plot

[kevin198930]

Hello,

I have visium data that I converted to an Anndata object using the stlearn workflow:

https://stlearn.readthedocs.io/en/latest/tutorials/Read_any_data.html

import stlearn as st
import pandas as pd
import numpy

count_matrix = pandas.read_csv("/Anndata_objects/s18_counts.csv")
spatial = pandas.read_csv("/Anndata_objects/s18_coordinates.csv")
metadata = pandas.read_csv("~/Anndata_objects/s18_metadata.csv")

adata = st.create_stlearn(count=count_matrix,spatial=spatial,library_id="s18", scale=1,background_color="white")
adata.obs["cell_type"] = numpy.asarray(metadata["celltype"])
adata.obs["cell_type"] = pd.Categorical(adata.obs["cell_type"]

print(adata)
AnnData object with n_obs × n_vars = 3064 × 14290
obs: 'imagecol', 'imagerow', 'cell_type'
uns: 'spatial'
obsm: 'spatial'

print(adata.obs['cell_type'])
0 Astro
1 Astro
2 Astro
3 Astro
4 Astro
...
3059 Astro
3060 Astro
3061 Astro
3062 Astro
3063 Astro
Name: cell_type, Length: 3064, dtype: category
Categories (4, object): ['Astro', 'Inhib.neurons', 'OC-like', 'Pericyte']

print(adata.obs['imagecol'])
print(adata.obs['imagerow'])

0 9484
1 10932
2 3795
3 11225
4 8690
...
3059 6488
3060 10767
3061 11087
3062 8716
3063 2701
Name: imagecol, Length: 3064, dtype: int64
0 3721
1 11258
2 4467
3 4170
4 2543
...
3059 6003
3060 9169
3061 10258
3062 10539
3063 8378
Name: imagerow, Length: 3064, dtype: int64

When I try to then run st.pl.cluster_plot(adata, use_label='cell_type'), I get the following error:

---

TypeError Traceback (most recent call last)
in
----> 1 st.pl.cluster_plot(adata, use_label='cell_type')

/usr/local/python/lib/python3.9/site-packages/stlearn/plotting/cluster_plot.py in cluster_plot(adata, title, figsize, cmap, use_label, list_clusters, ax, fig, show_plot, show_axis, show_image, show_color_bar, zoom_coord, crop, margin, size, image_alpha, cell_alpha, fname, dpi, show_subcluster, show_cluster_labels, show_trajectories, reverse, show_node, threshold_spots, text_box_size, color_bar_size, bbox_to_anchor, trajectory_node_size, trajectory_alpha, trajectory_width, trajectory_edge_color, trajectory_arrowsize)
85 assert use_label != None, "Please select use_label parameter"
86
---> 87 ClusterPlot(
88 adata,
89 title=title,

/usr/local/python/lib/python3.9/site-packages/stlearn/plotting/classes.py in init(self, adata, title, figsize, cmap, use_label, list_clusters, ax, fig, show_plot, show_axis, show_image, show_color_bar, crop, zoom_coord, margin, size, image_alpha, cell_alpha, fname, dpi, show_subcluster, show_cluster_labels, show_trajectories, reverse, show_node, threshold_spots, text_box_size, color_bar_size, bbox_to_anchor, trajectory_node_size, trajectory_alpha, trajectory_width, trajectory_edge_color, trajectory_arrowsize)
659 trajectory_arrowsize: Optional[int] = 17,
660 ):
--> 661 super().init(
662 adata=adata,
663 title=title,

/usr/local/python/lib/python3.9/site-packages/stlearn/plotting/classes.py in init(self, adata, title, figsize, cmap, use_label, list_clusters, ax, fig, show_plot, show_axis, show_image, show_color_bar, color_bar_label, zoom_coord, crop, margin, size, image_alpha, cell_alpha, use_raw, fname, dpi, **kwds)
136 crop = False
137 if crop:
--> 138 self._crop_image(self.ax, margin)
139
140 def _select_clusters(self):

/usr/local/python/lib/python3.9/site-packages/stlearn/plotting/classes.py in _crop_image(self, main_ax, margin)
186 def _crop_image(self, main_ax: _AxesSubplot, margin: float):
187
--> 188 main_ax.set_xlim(self.imagecol.min() - margin, self.imagecol.max() + margin)
189
190 main_ax.set_ylim(self.imagerow.min() - margin, self.imagerow.max() + margin)

TypeError: unsupported operand type(s) for -: 'str' and 'int'

It seems the imagecol and imagerow are dtypes int64, I don't know if this is the dtype they are supposed to be. The cell_type obs is a category dtype. Any help would be greatly appreciated!