TypeError: Image data of dtype object cannot be converted to float for Response heatmap

[hyjforesight]

Hello Dynamo, I was running the Cell-wise analyses tutorial. It was smooth until the Response heatmap. I got a TypeError: Image data of dtype object cannot be converted to float. Appreciate it if you could help me with this issue. Thanks! Best, YJ

dyn.vf.jacobian(adata, regulators=["SPI1", "GATA1"], effectors=["SPI1", "GATA1"], sample_ncells=1000, basis='pca', Qkey='PCs', method='analytical')
dyn.pl.response(adata, pairs_mat=np.array([["SPI1", "GATA1"], ["GATA1", "SPI1"], ["SPI1", "SPI1"], ["GATA1", "GATA1"]]), ykey="jacobian", log=False, cmap=None, save_show_or_return="show")

Transforming subset Jacobian: 100%|██████████| 1947/1947 [00:00<00:00, 70465.44it/s]
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Input In [17], in <cell line: 4>()
      2 get_ipython().run_line_magic('matplotlib', 'inline')
      3 dyn.vf.jacobian(adata, regulators=["SPI1", "GATA1"], effectors=["SPI1", "GATA1"], sample_ncells=1000, basis='pca', Qkey='PCs', method='analytical')
----> 4 dyn.pl.response(adata, pairs_mat=np.array([["SPI1", "GATA1"], ["GATA1", "SPI1"], ["SPI1", "SPI1"], ["GATA1", "GATA1"]]), ykey="jacobian", log=False, cmap=None,
      5                 save_show_or_return="show")

File ~\anaconda3\envs\dynamo\lib\site-packages\dynamo\plot\heatmaps.py:420, in response(adata, pairs_mat, xkey, ykey, log, drop_zero_cells, delay, grid_num, n_row, n_col, cmap, show_ridge, show_rug, zero_indicator, zero_line_style, zero_line_width, mean_style, fit_curve, fit_mode, curve_style, curve_lw, no_degradation, show_extent, ext_format, stacked_fraction, figsize, save_show_or_return, save_kwargs, return_data)
    417 axins = inset_axes(axes[i, j], bbox_transform=axes[i, j].transAxes, **inset_dict)
    419 ext_lim = (min(x_val), max(x_val), min(y_val), max(y_val))
--> 420 im = axes[i, j].imshow(
    421     values,
    422     interpolation="mitchell",
    423     origin="lower",
    424     extent=ext_lim if show_extent else None,
    425     cmap=cmap,
    426 )
    427 cb = fig.colorbar(im, cax=axins)
    428 cb.set_alpha(1)

File ~\anaconda3\envs\dynamo\lib\site-packages\matplotlib\__init__.py:1361, in _preprocess_data.<locals>.inner(ax, data, *args, **kwargs)
   1358 @functools.wraps(func)
   1359 def inner(ax, *args, data=None, **kwargs):
   1360     if data is None:
-> 1361         return func(ax, *map(sanitize_sequence, args), **kwargs)
   1363     bound = new_sig.bind(ax, *args, **kwargs)
   1364     auto_label = (bound.arguments.get(label_namer)
   1365                   or bound.kwargs.get(label_namer))

File ~\anaconda3\envs\dynamo\lib\site-packages\matplotlib\axes\_axes.py:5609, in Axes.imshow(self, X, cmap, norm, aspect, interpolation, alpha, vmin, vmax, origin, extent, filternorm, filterrad, resample, url, **kwargs)
   5604 self.set_aspect(aspect)
   5605 im = mimage.AxesImage(self, cmap, norm, interpolation, origin, extent,
   5606                       filternorm=filternorm, filterrad=filterrad,
   5607                       resample=resample, **kwargs)
-> 5609 im.set_data(X)
   5610 im.set_alpha(alpha)
   5611 if im.get_clip_path() is None:
   5612     # image does not already have clipping set, clip to axes patch

File ~\anaconda3\envs\dynamo\lib\site-packages\matplotlib\image.py:700, in _ImageBase.set_data(self, A)
    696 self._A = cbook.safe_masked_invalid(A, copy=True)
    698 if (self._A.dtype != np.uint8 and
    699         not np.can_cast(self._A.dtype, float, "same_kind")):
--> 700     raise TypeError("Image data of dtype {} cannot be converted to "
    701                     "float".format(self._A.dtype))
    703 if self._A.ndim == 3 and self._A.shape[-1] == 1:
    704     # If just one dimension assume scalar and apply colormap
    705     self._A = self._A[:, :, 0]

TypeError: Image data of dtype object cannot be converted to float

[Xiaojieqiu]

@dummyindex can you take a look at this. I am busy this and next week

Also @hyjforesight feel free to dig into the source code more closely (somehow your data generated for the heatmap is object instead of float) and welcome to contribute.

[hyjforesight]

Hello @Xiaojieqiu and @dummyindex Thanks for the response and for helping me. Sorry, I'm not professional at coding. I can just report the errors that I met. Hope it also helps Dynamo. Thanks! Best, YJ

[stupidstupidstupidstupid]

I met the same issue too. Have you fixed it now? What should I do? Thank you very much. @dummyindex @Xiaojieqiu

[stupidstupidstupidstupid]

%matplotlib inline

dyn.vf.jacobian(adata_labeling, regulators=["SPI1", "GATA1"], effectors=["SPI1", "GATA1"]) dyn.pl.response( adata_labeling, np.array([["SPI1", "GATA1"], ["GATA1", "SPI1"], ["SPI1", "SPI1"], ["GATA1", "GATA1"]]), ykey="jacobian", log=False, drop_zero_cells=True, grid_num=25, figsize=(5, 3), save_show_or_return="show" )

TypeError Traceback (most recent call last) Input In [88], in <cell line: 4>() 1 get_ipython().run_line_magic('matplotlib', 'inline') 3 dyn.vf.jacobian(adata_labeling, regulators=["SPI1", "GATA1"], effectors=["SPI1", "GATA1"]) ----> 4 dyn.pl.response( 5 adata_labeling, 6 np.array([["SPI1", "GATA1"], ["GATA1", "SPI1"], ["SPI1", "SPI1"], ["GATA1", "GATA1"]]), 7 ykey="jacobian", 8 log=False, 9 drop_zero_cells=True, 10 grid_num=25, 11 figsize=(5, 3), 12 save_show_or_return="show" 13 )

File ~\AppData\Roaming\Python\Python39\site-packages\dynamo\plot\heatmaps.py:420, in response(adata, pairs_mat, xkey, ykey, log, drop_zero_cells, delay, grid_num, n_row, n_col, cmap, show_ridge, show_rug, zero_indicator, zero_line_style, zero_line_width, mean_style, fit_curve, fit_mode, curve_style, curve_lw, no_degradation, show_extent, ext_format, stacked_fraction, figsize, save_show_or_return, save_kwargs, return_data) 417 axins = inset_axes(axes[i, j], bbox_transform=axes[i, j].transAxes, **inset_dict) 419 ext_lim = (min(x_val), max(x_val), min(y_val), max(y_val)) --> 420 im = axes[i, j].imshow( 421 values, 422 interpolation="mitchell", 423 origin="lower", 424 extent=ext_lim if show_extent else None, 425 cmap=cmap, 426 ) 427 cb = fig.colorbar(im, cax=axins) 428 cb.set_alpha(1)

File ~\AppData\Roaming\Python\Python39\site-packages\matplotlib_init_.py:1361, in _preprocess_data..inner(ax, data, *args, **kwargs) 1358 @functools.wraps(func) 1359 def inner(ax, *args, data=None, **kwargs): 1360 if data is None: -> 1361 return func(ax, *map(sanitize_sequence, args), **kwargs) 1363 bound = new_sig.bind(ax, *args, **kwargs) 1364 auto_label = (bound.arguments.get(label_namer) 1365 or bound.kwargs.get(label_namer))

File ~\AppData\Roaming\Python\Python39\site-packages\matplotlib\axes_axes.py:5609, in Axes.imshow(self, X, cmap, norm, aspect, interpolation, alpha, vmin, vmax, origin, extent, filternorm, filterrad, resample, url, **kwargs) 5604 self.set_aspect(aspect) 5605 im = mimage.AxesImage(self, cmap, norm, interpolation, origin, extent, 5606 filternorm=filternorm, filterrad=filterrad, 5607 resample=resample, **kwargs) -> 5609 im.set_data(X) 5610 im.set_alpha(alpha) 5611 if im.get_clip_path() is None: 5612 # image does not already have clipping set, clip to axes patch

File ~\AppData\Roaming\Python\Python39\site-packages\matplotlib\image.py:700, in _ImageBase.set_data(self, A) 696 self._A = cbook.safe_masked_invalid(A, copy=True) 698 if (self._A.dtype != np.uint8 and 699 not np.can_cast(self._A.dtype, float, "same_kind")): --> 700 raise TypeError("Image data of dtype {} cannot be converted to " 701 "float".format(self._A.dtype)) 703 if self._A.ndim == 3 and self._A.shape[-1] == 1: 704 # If just one dimension assume scalar and apply colormap 705 self._A = self._A[:, :, 0]

TypeError: Image data of dtype object cannot be converted to float

[hyjforesight]

check https://github.com/aristoteleo/dynamo-release/issues/392