Fixed bug because of which extent of previous axs was not respected

[timtreis]

Fixesissue 100

[codecov-commenter]

Codecov Report

Merging #101 (cdf4382) into main (b84c1ab) will increase coverage by 5.83%.
The diff coverage is 87.87%.

Additional details and impacted files

@@ Coverage Diff @@## main #101 +/- ##
==========================================
+ Coverage 70.54% 76.37% +5.83% 
==========================================
Files 9 9 Lines 1117 1143 +26 ==========================================
+ Hits 788 873 +85 + Misses 329 270 -59 

Impacted Files	Coverage Δ
src/spatialdata_plot/pl/utils.py	63.40% <75.00%> (+7.11%)	⬆️
src/spatialdata_plot/pl/basic.py	83.88% <92.00%> (+0.55%)	⬆️

... and 2 files with indirect coverage changes

[timtreis]

@jefferyUstc, could you verify if the branch from this PR fixes your issue with the spatial_query notebook? You should be able to install it with

pip install -U git+https://github.com/scverse/spatialdata-plot.git@bugfix/issue100-get_extent-produces-wrong-output-after-spatial-query

[jefferyUstc]

@jefferyUstc, could you verify if the branch from this PR fixes your issue with the spatial_query notebook? You should be able to install it with

pip install -U git+https://github.com/scverse/spatialdata-plot.git@bugfix/issue100-get_extent-produces-wrong-output-after-spatial-query

thank you, I'll try ASAP.

[jefferyUstc]

Hi, generally it works now.
I re-rerun the tutorial codes:

[timtreis]

Thank you for pointing out the mismatch between plot and legend, I opened a new issue to address this: #104

What do you mean with your second annotation? The fact that the plot border overlaps the points at the edge? I added a pad_extent argument to the pl.show() function to combat this, if wanted. You can use it as follows:

f, ax = plt.subplots(figsize=(7, 7))
sdata_ST8059048.pl.render_shapes().pl.show(ax=ax)
cropped_sdata.pl.render_shapes(color="Sox2").pl.show(ax=ax, colorbar=True, pad_extent=50)
# show the spatial query bounding box
rect = patches.Rectangle((8000, 12000), 4000, 4000, linewidth=5, edgecolor="k", facecolor="none")
ax.add_patch(rect)

[timtreis]

Fixesissue 100

[codecov-commenter]

Codecov Report

Merging #101 (cdf4382) into main (b84c1ab) will increase coverage by 5.83%.
The diff coverage is 87.87%.

Additional details and impacted files

@@ Coverage Diff @@## main #101 +/- ##
==========================================
+ Coverage 70.54% 76.37% +5.83% 
==========================================
Files 9 9 Lines 1117 1143 +26 ==========================================
+ Hits 788 873 +85 + Misses 329 270 -59 

Impacted Files	Coverage Δ
src/spatialdata_plot/pl/utils.py	63.40% <75.00%> (+7.11%)	⬆️
src/spatialdata_plot/pl/basic.py	83.88% <92.00%> (+0.55%)	⬆️

... and 2 files with indirect coverage changes

[timtreis]

@jefferyUstc, could you verify if the branch from this PR fixes your issue with the spatial_query notebook? You should be able to install it with

pip install -U git+https://github.com/scverse/spatialdata-plot.git@bugfix/issue100-get_extent-produces-wrong-output-after-spatial-query

[jefferyUstc]

@jefferyUstc, could you verify if the branch from this PR fixes your issue with the spatial_query notebook? You should be able to install it with

pip install -U git+https://github.com/scverse/spatialdata-plot.git@bugfix/issue100-get_extent-produces-wrong-output-after-spatial-query

thank you, I'll try ASAP.

[jefferyUstc]

Hi, generally it works now.
I re-rerun the tutorial codes:

[timtreis]

Thank you for pointing out the mismatch between plot and legend, I opened a new issue to address this: #104

What do you mean with your second annotation? The fact that the plot border overlaps the points at the edge? I added a pad_extent argument to the pl.show() function to combat this, if wanted. You can use it as follows:

f, ax = plt.subplots(figsize=(7, 7))
sdata_ST8059048.pl.render_shapes().pl.show(ax=ax)
cropped_sdata.pl.render_shapes(color="Sox2").pl.show(ax=ax, colorbar=True, pad_extent=50)
# show the spatial query bounding box
rect = patches.Rectangle((8000, 12000), 4000, 4000, linewidth=5, edgecolor="k", facecolor="none")
ax.add_patch(rect)

[timtreis]

Fixesissue 100

[codecov-commenter]

Codecov Report

Merging #101 (cdf4382) into main (b84c1ab) will increase coverage by 5.83%.
The diff coverage is 87.87%.

Additional details and impacted files

@@ Coverage Diff @@## main #101 +/- ##
==========================================
+ Coverage 70.54% 76.37% +5.83% 
==========================================
Files 9 9 Lines 1117 1143 +26 ==========================================
+ Hits 788 873 +85 + Misses 329 270 -59 

Impacted Files	Coverage Δ
src/spatialdata_plot/pl/utils.py	63.40% <75.00%> (+7.11%)	⬆️
src/spatialdata_plot/pl/basic.py	83.88% <92.00%> (+0.55%)	⬆️

... and 2 files with indirect coverage changes

[timtreis]

@jefferyUstc, could you verify if the branch from this PR fixes your issue with the spatial_query notebook? You should be able to install it with

pip install -U git+https://github.com/scverse/spatialdata-plot.git@bugfix/issue100-get_extent-produces-wrong-output-after-spatial-query

[jefferyUstc]

@jefferyUstc, could you verify if the branch from this PR fixes your issue with the spatial_query notebook? You should be able to install it with

pip install -U git+https://github.com/scverse/spatialdata-plot.git@bugfix/issue100-get_extent-produces-wrong-output-after-spatial-query

thank you, I'll try ASAP.

[jefferyUstc]

Hi, generally it works now.
I re-rerun the tutorial codes:

[timtreis]

Thank you for pointing out the mismatch between plot and legend, I opened a new issue to address this: #104

What do you mean with your second annotation? The fact that the plot border overlaps the points at the edge? I added a pad_extent argument to the pl.show() function to combat this, if wanted. You can use it as follows:

f, ax = plt.subplots(figsize=(7, 7))
sdata_ST8059048.pl.render_shapes().pl.show(ax=ax)
cropped_sdata.pl.render_shapes(color="Sox2").pl.show(ax=ax, colorbar=True, pad_extent=50)
# show the spatial query bounding box
rect = patches.Rectangle((8000, 12000), 4000, 4000, linewidth=5, edgecolor="k", facecolor="none")
ax.add_patch(rect)

[timtreis]

Fixesissue 100

[codecov-commenter]

Codecov Report

Merging #101 (cdf4382) into main (b84c1ab) will increase coverage by 5.83%.
The diff coverage is 87.87%.

Additional details and impacted files

@@ Coverage Diff @@## main #101 +/- ##
==========================================
+ Coverage 70.54% 76.37% +5.83% 
==========================================
Files 9 9 Lines 1117 1143 +26 ==========================================
+ Hits 788 873 +85 + Misses 329 270 -59 

Impacted Files	Coverage Δ
src/spatialdata_plot/pl/utils.py	63.40% <75.00%> (+7.11%)	⬆️
src/spatialdata_plot/pl/basic.py	83.88% <92.00%> (+0.55%)	⬆️

... and 2 files with indirect coverage changes

[timtreis]

@jefferyUstc, could you verify if the branch from this PR fixes your issue with the spatial_query notebook? You should be able to install it with

pip install -U git+https://github.com/scverse/spatialdata-plot.git@bugfix/issue100-get_extent-produces-wrong-output-after-spatial-query

[jefferyUstc]

@jefferyUstc, could you verify if the branch from this PR fixes your issue with the spatial_query notebook? You should be able to install it with

pip install -U git+https://github.com/scverse/spatialdata-plot.git@bugfix/issue100-get_extent-produces-wrong-output-after-spatial-query

thank you, I'll try ASAP.

[jefferyUstc]

Hi, generally it works now.
I re-rerun the tutorial codes:

[timtreis]

Thank you for pointing out the mismatch between plot and legend, I opened a new issue to address this: #104

What do you mean with your second annotation? The fact that the plot border overlaps the points at the edge? I added a pad_extent argument to the pl.show() function to combat this, if wanted. You can use it as follows:

f, ax = plt.subplots(figsize=(7, 7))
sdata_ST8059048.pl.render_shapes().pl.show(ax=ax)
cropped_sdata.pl.render_shapes(color="Sox2").pl.show(ax=ax, colorbar=True, pad_extent=50)
# show the spatial query bounding box
rect = patches.Rectangle((8000, 12000), 4000, 4000, linewidth=5, edgecolor="k", facecolor="none")
ax.add_patch(rect)

[timtreis]

Fixesissue 100

[codecov-commenter]

Codecov Report

Merging #101 (cdf4382) into main (b84c1ab) will increase coverage by 5.83%.
The diff coverage is 87.87%.

Additional details and impacted files

@@ Coverage Diff @@## main #101 +/- ##
==========================================
+ Coverage 70.54% 76.37% +5.83% 
==========================================
Files 9 9 Lines 1117 1143 +26 ==========================================
+ Hits 788 873 +85 + Misses 329 270 -59 

Impacted Files	Coverage Δ
src/spatialdata_plot/pl/utils.py	63.40% <75.00%> (+7.11%)	⬆️
src/spatialdata_plot/pl/basic.py	83.88% <92.00%> (+0.55%)	⬆️

... and 2 files with indirect coverage changes

[timtreis]

@jefferyUstc, could you verify if the branch from this PR fixes your issue with the spatial_query notebook? You should be able to install it with

pip install -U git+https://github.com/scverse/spatialdata-plot.git@bugfix/issue100-get_extent-produces-wrong-output-after-spatial-query

[jefferyUstc]

@jefferyUstc, could you verify if the branch from this PR fixes your issue with the spatial_query notebook? You should be able to install it with

pip install -U git+https://github.com/scverse/spatialdata-plot.git@bugfix/issue100-get_extent-produces-wrong-output-after-spatial-query

thank you, I'll try ASAP.

[jefferyUstc]

Hi, generally it works now.
I re-rerun the tutorial codes:

[timtreis]

Thank you for pointing out the mismatch between plot and legend, I opened a new issue to address this: #104

What do you mean with your second annotation? The fact that the plot border overlaps the points at the edge? I added a pad_extent argument to the pl.show() function to combat this, if wanted. You can use it as follows:

f, ax = plt.subplots(figsize=(7, 7))
sdata_ST8059048.pl.render_shapes().pl.show(ax=ax)
cropped_sdata.pl.render_shapes(color="Sox2").pl.show(ax=ax, colorbar=True, pad_extent=50)
# show the spatial query bounding box
rect = patches.Rectangle((8000, 12000), 4000, 4000, linewidth=5, edgecolor="k", facecolor="none")
ax.add_patch(rect)

[timtreis]

Fixesissue 100

[codecov-commenter]

Codecov Report

Merging #101 (cdf4382) into main (b84c1ab) will increase coverage by 5.83%.
The diff coverage is 87.87%.

Additional details and impacted files

@@ Coverage Diff @@## main #101 +/- ##
==========================================
+ Coverage 70.54% 76.37% +5.83% 
==========================================
Files 9 9 Lines 1117 1143 +26 ==========================================
+ Hits 788 873 +85 + Misses 329 270 -59 

Impacted Files	Coverage Δ
src/spatialdata_plot/pl/utils.py	63.40% <75.00%> (+7.11%)	⬆️
src/spatialdata_plot/pl/basic.py	83.88% <92.00%> (+0.55%)	⬆️

... and 2 files with indirect coverage changes

[timtreis]

@jefferyUstc, could you verify if the branch from this PR fixes your issue with the spatial_query notebook? You should be able to install it with

pip install -U git+https://github.com/scverse/spatialdata-plot.git@bugfix/issue100-get_extent-produces-wrong-output-after-spatial-query

[jefferyUstc]

@jefferyUstc, could you verify if the branch from this PR fixes your issue with the spatial_query notebook? You should be able to install it with

pip install -U git+https://github.com/scverse/spatialdata-plot.git@bugfix/issue100-get_extent-produces-wrong-output-after-spatial-query

thank you, I'll try ASAP.

[jefferyUstc]

Hi, generally it works now.
I re-rerun the tutorial codes:

[timtreis]

Thank you for pointing out the mismatch between plot and legend, I opened a new issue to address this: #104

What do you mean with your second annotation? The fact that the plot border overlaps the points at the edge? I added a pad_extent argument to the pl.show() function to combat this, if wanted. You can use it as follows:

f, ax = plt.subplots(figsize=(7, 7))
sdata_ST8059048.pl.render_shapes().pl.show(ax=ax)
cropped_sdata.pl.render_shapes(color="Sox2").pl.show(ax=ax, colorbar=True, pad_extent=50)
# show the spatial query bounding box
rect = patches.Rectangle((8000, 12000), 4000, 4000, linewidth=5, edgecolor="k", facecolor="none")
ax.add_patch(rect)

[timtreis]

Fixesissue 100

[codecov-commenter]

Codecov Report

Merging #101 (cdf4382) into main (b84c1ab) will increase coverage by 5.83%.
The diff coverage is 87.87%.

Additional details and impacted files

@@ Coverage Diff @@## main #101 +/- ##
==========================================
+ Coverage 70.54% 76.37% +5.83% 
==========================================
Files 9 9 Lines 1117 1143 +26 ==========================================
+ Hits 788 873 +85 + Misses 329 270 -59 

Impacted Files	Coverage Δ
src/spatialdata_plot/pl/utils.py	63.40% <75.00%> (+7.11%)	⬆️
src/spatialdata_plot/pl/basic.py	83.88% <92.00%> (+0.55%)	⬆️

... and 2 files with indirect coverage changes

[timtreis]

@jefferyUstc, could you verify if the branch from this PR fixes your issue with the spatial_query notebook? You should be able to install it with

pip install -U git+https://github.com/scverse/spatialdata-plot.git@bugfix/issue100-get_extent-produces-wrong-output-after-spatial-query

[jefferyUstc]

@jefferyUstc, could you verify if the branch from this PR fixes your issue with the spatial_query notebook? You should be able to install it with

pip install -U git+https://github.com/scverse/spatialdata-plot.git@bugfix/issue100-get_extent-produces-wrong-output-after-spatial-query

thank you, I'll try ASAP.

[jefferyUstc]

Hi, generally it works now.
I re-rerun the tutorial codes:

[timtreis]

Thank you for pointing out the mismatch between plot and legend, I opened a new issue to address this: #104

What do you mean with your second annotation? The fact that the plot border overlaps the points at the edge? I added a pad_extent argument to the pl.show() function to combat this, if wanted. You can use it as follows:

f, ax = plt.subplots(figsize=(7, 7))
sdata_ST8059048.pl.render_shapes().pl.show(ax=ax)
cropped_sdata.pl.render_shapes(color="Sox2").pl.show(ax=ax, colorbar=True, pad_extent=50)
# show the spatial query bounding box
rect = patches.Rectangle((8000, 12000), 4000, 4000, linewidth=5, edgecolor="k", facecolor="none")
ax.add_patch(rect)

[timtreis]

Fixesissue 100

[codecov-commenter]

Codecov Report

Merging #101 (cdf4382) into main (b84c1ab) will increase coverage by 5.83%.
The diff coverage is 87.87%.

Additional details and impacted files

@@ Coverage Diff @@## main #101 +/- ##
==========================================
+ Coverage 70.54% 76.37% +5.83% 
==========================================
Files 9 9 Lines 1117 1143 +26 ==========================================
+ Hits 788 873 +85 + Misses 329 270 -59 

Impacted Files	Coverage Δ
src/spatialdata_plot/pl/utils.py	63.40% <75.00%> (+7.11%)	⬆️
src/spatialdata_plot/pl/basic.py	83.88% <92.00%> (+0.55%)	⬆️

... and 2 files with indirect coverage changes

[timtreis]

@jefferyUstc, could you verify if the branch from this PR fixes your issue with the spatial_query notebook? You should be able to install it with

pip install -U git+https://github.com/scverse/spatialdata-plot.git@bugfix/issue100-get_extent-produces-wrong-output-after-spatial-query

[jefferyUstc]

@jefferyUstc, could you verify if the branch from this PR fixes your issue with the spatial_query notebook? You should be able to install it with

pip install -U git+https://github.com/scverse/spatialdata-plot.git@bugfix/issue100-get_extent-produces-wrong-output-after-spatial-query

thank you, I'll try ASAP.

[jefferyUstc]

Hi, generally it works now.
I re-rerun the tutorial codes:

[timtreis]

Thank you for pointing out the mismatch between plot and legend, I opened a new issue to address this: #104

What do you mean with your second annotation? The fact that the plot border overlaps the points at the edge? I added a pad_extent argument to the pl.show() function to combat this, if wanted. You can use it as follows:

f, ax = plt.subplots(figsize=(7, 7))
sdata_ST8059048.pl.render_shapes().pl.show(ax=ax)
cropped_sdata.pl.render_shapes(color="Sox2").pl.show(ax=ax, colorbar=True, pad_extent=50)
# show the spatial query bounding box
rect = patches.Rectangle((8000, 12000), 4000, 4000, linewidth=5, edgecolor="k", facecolor="none")
ax.add_patch(rect)