Comments (11)
li1311139481
commented on August 19, 2024
Hi; anyone can help ?
from gseapy.
chrissymkcn
commented on August 19, 2024
I am experiencing the same issue with gseapy '1.0.4' even with more than 15 top terms, have tried:
converting the column to plot (FDR q-val) to np.float64
plotting other pval columns
from gseapy.
li1311139481
commented on August 19, 2024
@chrissymkcn Thanks. I tried, but not work
from gseapy.
li1311139481
commented on August 19, 2024
I solve the problem:
3.10.12 | packaged by conda-forge | (main, Jun 23 2023, 22:40:32) [GCC 12.3.0]
CPython
Linux-3.10.0-514.21.1.el7.x86_64-x86_64-with-glibc2.17
1.0.4
pre_res = gp.prerank(rnk=rnk, gene_sets=gene_sets, threads=8,
permutation_num=1000, no_plot=True, max_size=1000, min_size=5)
res = pre_res.res2d
res.index = res["Term"]
res['abs_NES'] = res['NES'].abs()
res_plot = res.sort_values(by=["FDR q-val", 'FWER p-val', 'abs_NES'],
ascending=[True, True, False], inplace=False, ignore_index=True).head(15)
res_plot = res_plot.sort_values(
by=['NES'], ascending=[True], ignore_index=True)
if max(res_plot["FDR q-val"]) <= 0.05:
dotplot(res_plot, column="FDR q-val", top_term=15, y_order=list(
res_plot["Term"]), ofname=f'{out_file}/GSEA.{gs_name}.dotplot.pdf')
elif max(res_plot["FDR q-val"]) > 0.05:
dotplot(
res_plot,
column="FDR q-val",
cutoff=max(res_plot["FDR q-val"]),
y_order=list(res_plot["Term"]),
top_term=15, ofname=f'{out_file}/GSEA.{gs_name}.dotplot.pdf'
)
Thanks
from gseapy.
li1311139481
commented on August 19, 2024
Sorry to reopen the question, the problem still exists.
Although I have found a solution, I don't think it is the best way. So I reopened the question. Who has a better way?
3.10.12 | packaged by conda-forge | (main, Jun 23 2023, 22:40:32) [GCC 12.3.0]
CPython
Linux-3.10.0-514.21.1.el7.x86_64-x86_64-with-glibc2.17
1.0.4
print(res_plot)
| Unnamed: 0 | Name | Term | ES | NES | NOM p-val | FDR q-val | FWER p-val | Tag % | Gene % | Lead_genes | abs_NES | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 14 | prerank | MANNO_MIDBRAIN_NEUROTYPES_HPROGFPM | 0.758843 | 3.383383 | 0.0 | 0.0 | 0.0 | 117/182 | 12.66% | TTK;PTGR1;FOXM1;GINS1;GAS2;RFC4;PLK1;PBK;SPAG5... | 3.383383 |
| 1 | 13 | prerank | FAN_EMBRYONIC_CTX_MICROGLIA_1 | 0.820998 | 3.410072 | 0.0 | 0.0 | 0.0 | 87/122 | 10.51% | TTK;FOXM1;PLK1;PBK;SPAG5;FBXO5;SPC25;KIF2C;SHC... | 3.410072 |
| 2 | 12 | prerank | HSD17B8_TARGET_GENES | 0.719642 | 3.424900 | 0.0 | 0.0 | 0.0 | 170/329 | 11.98% | TTK;EXO1;FOXM1;UNG;PSMC3IP;SYCE2;DTL;GINS1;MYB... | 3.424900 |
| 3 | 11 | prerank | MANNO_MIDBRAIN_NEUROTYPES_HPROGBP | 0.784367 | 3.432844 | 0.0 | 0.0 | 0.0 | 104/152 | 9.91% | TTK;FOXM1;GINS1;MYBL2;SAPCD2;RFC4;PLK1;PBK;SPA... | 3.432844 |
| 4 | 10 | prerank | FAN_EMBRYONIC_CTX_NSC_2 | 0.776916 | 3.441287 | 0.0 | 0.0 | 0.0 | 122/187 | 12.66% | TUBB6;TTK;FOXM1;GINS1;SAPCD2;PLK1;PBK;SKA1;POC... | 3.441287 |
| 5 | 9 | prerank | ROSTY_CERVICAL_CANCER_PROLIFERATION_CLUSTER | 0.843112 | 3.486187 | 0.0 | 0.0 | 0.0 | 86/113 | 10.51% | TTK;FOXM1;DTL;GINS1;MYBL2;PLK1;CDC6;PBK;SPAG5;... | 3.486187 |
| 6 | 8 | prerank | ZHONG_PFC_C1_OPC | 0.794613 | 3.498902 | 0.0 | 0.0 | 0.0 | 126/175 | 12.66% | TUBB6;TTK;FOXM1;PLK1;PBK;SKA1;POC1A;SPAG5;TRIP... | 3.498902 |
| 7 | 7 | prerank | BLANCO_MELO_BRONCHIAL_EPITHELIAL_CELLS_INFLUEN... | 0.848646 | 3.501563 | 0.0 | 0.0 | 0.0 | 90/104 | 11.99% | TTK;EXO1;FOXM1;DTL;MYBL2;PLK1;CDC6;SKA1;SPAG5;... | 3.501563 |
| 8 | 6 | prerank | KOBAYASHI_EGFR_SIGNALING_24HR_DN | 0.791011 | 3.502551 | 0.0 | 0.0 | 0.0 | 128/185 | 10.80% | TUBB6;TTK;EXO1;UNG;PSMC3IP;DTL;RAD54B;GINS1;MY... | 3.502551 |
| 9 | 5 | prerank | GSE13547_CTRL_VS_ANTI_IGM_STIM_BCELL_12H_UP | 0.810430 | 3.536394 | 0.0 | 0.0 | 0.0 | 112/161 | 10.28% | TTK;PTGR1;SYCE2;GINS1;FIGNL1;PLK1;CDC6;PBK;SKA... | 3.536394 |
| 10 | 4 | prerank | GSE15750_DAY6_VS_DAY10_EFF_CD8_TCELL_UP | 0.817446 | 3.556787 | 0.0 | 0.0 | 0.0 | 113/158 | 10.51% | TTK;AUNIP;RAD54B;GINS1;MYBL2;FIGNL1;DSCC1;PLK1... | 3.556787 |
| 11 | 3 | prerank | GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_UP | 0.745410 | 3.598120 | 0.0 | 0.0 | 0.0 | 239/399 | 11.78% | SERPINE2;TTK;PTGR1;SUV39H2;EXO1;FOXM1;UNG;PSMC... | 3.598120 |
| 12 | 2 | prerank | DUTERTRE_ESTRADIOL_RESPONSE_24HR_UP | 0.797213 | 3.604187 | 0.0 | 0.0 | 0.0 | 159/213 | 12.70% | TTK;SUV39H2;EXO1;FOXM1;UNG;PSMC3IP;DTL;RAD54B;... | 3.604187 |
| 13 | 1 | prerank | FLORIO_NEOCORTEX_BASAL_RADIAL_GLIA_DN | 0.857793 | 3.605230 | 0.0 | 0.0 | 0.0 | 96/117 | 10.51% | TUBB6;TTK;EXO1;FOXM1;DTL;GINS1;MYBL2;PLK1;PBK;... | 3.605230 |
| 14 | 0 | prerank | GSE15750_DAY6_VS_DAY10_TRAF6KO_EFF_CD8_TCELL_UP | 0.846334 | 3.644140 | 0.0 | 0.0 | 0.0 | 122/155 | 10.65% | TTK;PTGR1;EXO1;FOXM1;MLF1;AUNIP;DTL;MYBL2;PLK1... | 3.644140 |
dotplot(
res_plot,
column="FDR q-val",
top_term=15,
y_order=list(res_plot["Term"]),
ofname=f"{out_file}/GSEA.msigdb.dotplot.pdf",
)
---------------------------------------------------------------------------
IntCastingNaNError Traceback (most recent call last)
Cell In[23], [line 1](vscode-notebook-cell:?execution_count=23&line=1)
----> [1](vscode-notebook-cell:?execution_count=23&line=1) dotplot(
[2](vscode-notebook-cell:?execution_count=23&line=2) res_plot,
[3](vscode-notebook-cell:?execution_count=23&line=3) column="FDR q-val",
[4](vscode-notebook-cell:?execution_count=23&line=4) # top_term=15,
[5](vscode-notebook-cell:?execution_count=23&line=5) # y_order=list(res_plot["Term"]),
[6](vscode-notebook-cell:?execution_count=23&line=6) # ofname=f"{out_file}/GSEA.msigdb.dotplot.pdf",
[7](vscode-notebook-cell:?execution_count=23&line=7) )
File /cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/gseapy/plot.py:1057, in dotplot(df, column, x, y, x_order, y_order, title, cutoff, top_term, size, figsize, cmap, ofname, xticklabels_rot, yticklabels_rot, marker, show_ring, **kwargs)
[1039](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/gseapy/plot.py:1039) return
[1041](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/gseapy/plot.py:1041) dot = DotPlot(
[1042](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/gseapy/plot.py:1042) df=df,
[1043](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/gseapy/plot.py:1043) x=x,
(...)
[1055](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/gseapy/plot.py:1055) marker=marker,
[1056](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/gseapy/plot.py:1056) )
-> [1057](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/gseapy/plot.py:1057) ax = dot.scatter(outer_ring=show_ring)
[1059](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/gseapy/plot.py:1059) if xticklabels_rot:
[1060](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/gseapy/plot.py:1060) for label in ax.get_xticklabels():
File /cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/gseapy/plot.py:731, in DotPlot.scatter(self, outer_ring)
[722](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/gseapy/plot.py:722) # scatter colormap range
[723](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/gseapy/plot.py:723) # df = df.assign(colmap=self.data[self.colname].round().astype("int"))
[724](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/gseapy/plot.py:724) # make area bigger to better visualization
[725](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/gseapy/plot.py:725) # area = df["Hits_ratio"] * plt.rcParams["lines.linewidth"] * 100
[726](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/gseapy/plot.py:726) df = self.data.assign(
[727](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/gseapy/plot.py:727) area=(
[728](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/gseapy/plot.py:728) self.data["Hits_ratio"] * self.scale * plt.rcParams["lines.markersize"]
[729](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/gseapy/plot.py:729) ).pow(2)
[730](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/gseapy/plot.py:730) )
--> [731](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/gseapy/plot.py:731) colmap = df[self.colname].astype(int)
[732](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/gseapy/plot.py:732) vmin = np.percentile(colmap.min(), 2)
[733](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/gseapy/plot.py:733) vmax = np.percentile(colmap.max(), 98)
File /cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/generic.py:5815, in NDFrame.astype(self, dtype, copy, errors)
[5808](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/generic.py:5808) results = [
[5809](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/generic.py:5809) self.iloc[:, i].astype(dtype, copy=copy)
[5810](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/generic.py:5810) for i in range(len(self.columns))
[5811](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/generic.py:5811) ]
[5813](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/generic.py:5813) else:
[5814](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/generic.py:5814) # else, only a single dtype is given
-> [5815](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/generic.py:5815) new_data = self._mgr.astype(dtype=dtype, copy=copy, errors=errors)
[5816](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/generic.py:5816) return self._constructor(new_data).__finalize__(self, method="astype")
[5818](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/generic.py:5818) # GH 33113: handle empty frame or series
File /cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/internals/managers.py:418, in BaseBlockManager.astype(self, dtype, copy, errors)
[417](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/internals/managers.py:417) def astype(self: T, dtype, copy: bool = False, errors: str = "raise") -> T:
--> [418](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/internals/managers.py:418) return self.apply("astype", dtype=dtype, copy=copy, errors=errors)
File /cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/internals/managers.py:327, in BaseBlockManager.apply(self, f, align_keys, ignore_failures, **kwargs)
[325](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/internals/managers.py:325) applied = b.apply(f, **kwargs)
[326](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/internals/managers.py:326) else:
--> [327](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/internals/managers.py:327) applied = getattr(b, f)(**kwargs)
[328](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/internals/managers.py:328) except (TypeError, NotImplementedError):
[329](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/internals/managers.py:329) if not ignore_failures:
File /cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/internals/blocks.py:591, in Block.astype(self, dtype, copy, errors)
[573](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/internals/blocks.py:573) """
[574](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/internals/blocks.py:574) Coerce to the new dtype.
[575](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/internals/blocks.py:575)
(...)
[587](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/internals/blocks.py:587) Block
[588](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/internals/blocks.py:588) """
[589](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/internals/blocks.py:589) values = self.values
--> [591](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/internals/blocks.py:591) new_values = astype_array_safe(values, dtype, copy=copy, errors=errors)
[593](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/internals/blocks.py:593) new_values = maybe_coerce_values(new_values)
[594](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/internals/blocks.py:594) newb = self.make_block(new_values)
File /cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/dtypes/cast.py:1309, in astype_array_safe(values, dtype, copy, errors)
[1306](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/dtypes/cast.py:1306) dtype = pandas_dtype(dtype)
[1308](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/dtypes/cast.py:1308) try:
-> [1309](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/dtypes/cast.py:1309) new_values = astype_array(values, dtype, copy=copy)
[1310](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/dtypes/cast.py:1310) except (ValueError, TypeError):
[1311](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/dtypes/cast.py:1311) # e.g. astype_nansafe can fail on object-dtype of strings
[1312](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/dtypes/cast.py:1312) # trying to convert to float
[1313](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/dtypes/cast.py:1313) if errors == "ignore":
File /cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/dtypes/cast.py:1257, in astype_array(values, dtype, copy)
[1254](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/dtypes/cast.py:1254) values = values.astype(dtype, copy=copy)
[1256](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/dtypes/cast.py:1256) else:
-> [1257](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/dtypes/cast.py:1257) values = astype_nansafe(values, dtype, copy=copy)
[1259](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/dtypes/cast.py:1259) # in pandas we don't store numpy str dtypes, so convert to object
[1260](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/dtypes/cast.py:1260) if isinstance(dtype, np.dtype) and issubclass(values.dtype.type, str):
File /cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/dtypes/cast.py:1168, in astype_nansafe(arr, dtype, copy, skipna)
[1165](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/dtypes/cast.py:1165) raise TypeError(f"cannot astype a timedelta from [{arr.dtype}] to [{dtype}]")
[1167](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/dtypes/cast.py:1167) elif np.issubdtype(arr.dtype, np.floating) and np.issubdtype(dtype, np.integer):
-> [1168](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/dtypes/cast.py:1168) return astype_float_to_int_nansafe(arr, dtype, copy)
[1170](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/dtypes/cast.py:1170) elif is_object_dtype(arr):
[1171](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/dtypes/cast.py:1171)
[1172](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/dtypes/cast.py:1172) # work around NumPy brokenness, #1987
[1173](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/dtypes/cast.py:1173) if np.issubdtype(dtype.type, np.integer):
File /cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/dtypes/cast.py:1213, in astype_float_to_int_nansafe(values, dtype, copy)
[1209](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/dtypes/cast.py:1209) """
[1210](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/dtypes/cast.py:1210) astype with a check preventing converting NaN to an meaningless integer value.
[1211](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/dtypes/cast.py:1211) """
[1212](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/dtypes/cast.py:1212) if not np.isfinite(values).all():
-> [1213](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/dtypes/cast.py:1213) raise IntCastingNaNError(
[1214](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/dtypes/cast.py:1214) "Cannot convert non-finite values (NA or inf) to integer"
[1215](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/dtypes/cast.py:1215) )
[1216](https://vscode-remote+ssh-002dremote-002b172-002e19-002e247-002e27.vscode-resource.vscode-cdn.net/cluster/facility/hlhuang/miniconda3/envs/py/lib/python3.10/site-packages/pandas/core/dtypes/cast.py:1216) return values.astype(dtype, copy=copy)
IntCastingNaNError: Cannot convert non-finite values (NA or inf) to integer
I find that the reason for the error is that all my FDR q-val is 0, and if I assign a p-value to something else, it works. I guess this is because we need to provide a range for the FDR q-val value in order to produce a gradient color.
For example:
res_plot.loc[14, ["FDR q-val"]] = 0.00001
dotplot(
res_plot,
column="FDR q-val",
cutoff=max(res_plot["FDR q-val"]),
y_order=list(res_plot["Term"]),
top_term=15
)
Another example
res_plot.loc[0, ["FDR q-val"]] = 1e-20
res_plot.loc[14, ["FDR q-val"]] = 1e-5
dotplot(
res_plot,
column="FDR q-val",
cutoff=max(res_plot["FDR q-val"]),
y_order=list(res_plot["Term"]),
top_term=15,
)
The range of color bars is the same as the value I specified, so my guess should be correct
Next, I did this in order to draw smoothly in the automated pipeline, although I know that this is not an accurate representation of the real FDR q-val, but it is enough for the plotting.
if res_plot["FDR q-val"].sum() == 0:
import numpy as np
rank = np.arange(len(res_plot))
min_val = 1e-9
max_val = 1e-8
values = min_val + (max_val - min_val) * (rank / (len(rank) - 1))
res_plot["FDR q-val"] = values
dotplot(
res_plot,
column="FDR q-val",
cutoff=max(res_plot["FDR q-val"]),
y_order=list(res_plot["Term"]),
top_term=15,
)
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zqfang
commented on August 19, 2024
I will try to investigate this. I just don't have enough time recently, sorry
Can you share me your data frame output? you can email it to me if you don't want to post it here
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chrissymkcn
commented on August 19, 2024
Mean while another workaround there is I think you can plot more terms (if you have) and export as svg and then adjust the graph manually if really necessary
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li1311139481
commented on August 19, 2024
@zqfang
Thank you for your reply, you don't have to apologize for it, we should thank you for your work
This is my original data frame.
GSEA.msigdb.stats.csv
If you want to know what did, That's my pre-process code
res = pd.read_csv(
GSEA.msigdb.stats.csv"
)
res.index = res["Term"]
res["abs_NES"] = res["NES"].abs()
res_plot = res.sort_values(
by=["FDR q-val", "FWER p-val", "abs_NES"],
ascending=[True, True, False],
inplace=False,
ignore_index=True,
).head(15)
res_plot = res_plot.sort_values(by=["NES"], ascending=[True], ignore_index=True)
if res_plot["FDR q-val"].sum() == 0:
import numpy as np
rank = np.arange(len(res_plot))
min_val = 1e-9
max_val = 1e-8
values = min_val + (max_val - min_val) * (rank / (len(rank) - 1))
res_plot["FDR q-val"] = values
dotplot(
res_plot,
column="FDR q-val",
cutoff=max(res_plot["FDR q-val"]),
y_order=list(res_plot["Term"]),
top_term=15,
)
from gseapy.
li1311139481
commented on August 19, 2024
Mean while another workaround there is I think you can plot more terms (if you have) and export as svg and then adjust the graph manually if really necessary
Haha, the slowest way, but actually the fastest way, and since I'm so obsessed with automation, I've been spending quite a bit of time on it
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zqfang
commented on August 19, 2024
@li1311139481 , so the initial issue for the dotplot is missing color values from the column FDR:
- Please ensure that the
colormapcolumn in your data frame does not consist entirely of zeros. ( this is where the bug is)- internally, the function will replace 0s with the lowest Pval, FDR values in your dataframe for visualization purpose).
- I added a value check to help user input appropriate data (for example, when you subset the first 15 rows, they are all 0s).
- the second issue for the NES order in the x-axis, it's fixed now
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li1311139481
commented on August 19, 2024
@zqfang.
OK. Thanks for your help. I'll be waiting for updates in the next version of conda.
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