Python Forum

Hello all,

I am stuck with the implementation of slicing dataframes within a custom function. I have looked on the internet and cannot find anything that is helping me :( any help would be much appreciated!

I am simply wrapping generating a umap and plotting it in seaborn into a wrapper function to avoid so much repeated code writing!

the function is as follows:

def activationUMAP(activations,dataIndex,ulMetric, ulVerbose, encodedMetadata, categoricalIndex,categoricalString, snsHue,snsPallete, snsLegend,ulNneighbour=40):

#subset layerouput to specific neuron activations (organ age etc)

    layer_outputpd=pd.DataFrame(activations, index=dataIndex.index)

    layer_outputCategory=[b]layer_outputpd.iloc[:,categoricalIndex][/b]
    layer_outputCategory.shape

    ##umap algorithm:: umap-learn

    layout = umap.UMAP(verbose=ulVerbose,metric=ulMetric,n_neighbors=ulNneighbour).fit_transform(layer_outputCategory)
    layout = normalize_layout(layout)

    subsetxtrain=encodedMetadata[encodedMetadata.index.isin(dataIndex.index)]
    subsetxtrain=subsetxtrain.reindex(layer_outputCategory.index)

    ##make umap layout above pandas df

    layout1=pd.DataFrame(layout)

    layout1[categoricalString] = subsetxtrain[categoricalString].values


    ##plot with seaborn

    umapPlot = sns.scatterplot(x=layout1.iloc[:,0], y=layout1.iloc[:,1], 
    data=layout1,hue=snsHue, palette=snsPallete, legend=snsLegend)
    umapPlot.legend()

    return(umapPlot)

I have highlighted in bold where the problem lies. when carrying out normal slicing, i would simply add :,0:12 or :,12:19 etc... to selectively chose different columns that belong to different classes... I have passed however the "categoricalIndex" argument so that in the function arguments, 0:12, 12:19 can simply be inserted, however this consistently provides an error as follows:

activationUMAP(activations=layer_output,dataIndex=X_train,
encodedMetadata=metadataencode,categoricalString="Organ", [b]categoricalIndex=0:12[/b],
ulMetric="euclidean", ulVerbose=True,snsHue="Organ",snsPallete="rainbow",snsLegend="brief")

this produces the following error:
File "", line 3
encodedMetadata=metadataencode,categoricalString="Organ", categoricalIndex=0:12,
^
SyntaxError: invalid syntax

I have tried different variations including removing the square brackets from the function etc.. and this still produces the same error. Note: if i simply pass :,0:12 within the actual function and remove the categoricalIndex argument, all works fine as it should! I really need this slicing argument however!

any help would be much appreciated! thank you!

Passing 0:12 as an argument value to a function definitely isn't valid Python syntax. Try categoricalIndex=slice(0, 12) instead.

(Mar-03-2020, 01:11 PM)scidam Wrote: [ -> ]Passing 0:12 as an argument value to a function definitely isn't valid Python syntax. Try categoricalIndex=slice(0, 12) instead.

this works PERFECTLY!! thank you so much!