GSEApy plot TypeError
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2
Entering edit mode
7 months ago
Emily ▴ 70

I'm using GSEApy to do my enrichment analysis. I sorted my pre_res based on nes. I was trying to get GSEA plot for the first term, which is the most enriched. The most enriched was 'Mitotic G2/M Transition Checkpoint (GO:0044818)'. Here is the code I attempted to generate the plot

gseaplot(pre_res.ranking,
         term='Mitotic G2/M Transition Checkpoint (GO:0044818)',
         **pre_res.results['Mitotic G2/M Transition Checkpoint (GO:0044818)'])

It gave me an error message saying this:

TypeError                                 Traceback (most recent call last)
Cell In[53], line 2
      1 # GSEA Plot
----> 2 gseaplot(pre_res.ranking,
      3          term='Mitotic G2/M Transition Checkpoint (GO:0044818)',
      4          **pre_res.results['Mitotic G2/M Transition Checkpoint (GO:0044818)'])

TypeError: gseaplot() got multiple values for argument 'term'

I even looked at the documentation but I'm not sure why it is giving me TypeError. Do I need to add something in the term=? Any help is much appreciated. Thank you.

gsea python DEG • 893 views
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1
Entering edit mode
7 months ago
Mark ★ 1.5k

There's something odd with your syntax. This is odd:

**pre_res.results['Mitotic G2/M Transition Checkpoint (GO:0044818)']

** only works in functions (kwargs). To unpack an object use *object.

Looking at this example:

# or use this to have more control on the plot
# from gseapy import gseaplot2
# terms = pre_res.res2d.Term[1:5]
# hits = [pre_res.results[t]['hits'] for t in terms]
# runes = [pre_res.results[t]['RES'] for t in terms]
# fig = gseaplot2(terms=terms, ress=runes, hits=hits,
#               rank_metric=gs_res.ranking,
#               legend_kws={'loc': (1.2, 0)}, # set the legend loc
#               figsize=(4,5)) # rank_metric=pre_res.ranking

If you want to specify many term then you need to provide the input as a list. The easiest way to do this is like this:

terms=['Mitotic G2/M Transition Checkpoint (GO:0044818)',
'Mitotic G2/M Transition Checkpoint (GO:0044818)']

Note the use of square brackets [ and ] to create a list. This is a python short hand syntax.

Your code to run the plot should look like this:

gseaplot(pre_res.ranking, term=terms)

Hope that helps

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1
Entering edit mode
6 months ago
John ▴ 10

Maybe you can try this:

gseaplot(term='Mitotic G2/M Transition Checkpoint (GO:0044818)', **pre_res.results['Mitotic G2/M Transition Checkpoint (GO:0044818)'])
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