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From dataframe #972

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mortonjt opened this issue Jun 14, 2024 · 0 comments
Open

From dataframe #972

mortonjt opened this issue Jun 14, 2024 · 0 comments

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@mortonjt
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One of the most common conversions to biom tables is from pandas data frames. Thus, having a Table.from_dataframe command would be a strong utility. As a first pass, the following can be done

@staticmethod
def from_dataframe(self, df):
    """ pd.DataFrame with rows as samples and features as columns. """
    return biom.Table(df.values.T, df.columns, df.index)

I find myself copying / pasting this command quite often. So having this embedded within biom would be low hanging fruit, but slightly ease analysis effort.

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