running time unlimited?

[KunHHE]

Hi @JuliaS92 Thanks for developing this tool. I noticed the running time is forever which is not normal I think? For example:

ProteinGroups = pd.read_csv('C:/Users/hekun/Downloads/proteinGroupsDemo.txt',low_memory=False, sep = '\t')

ProteinGroups = ProteinGroups.set_index('Protein IDs')

ProteinGroups.info() ProteinGroups = ProteinGroups[~ProteinGroups['Protein IDs'].str.contains("CON_")] ProteinGroups = ProteinGroups[~ProteinGroups['Protein IDs'].str.contains("REV__")] ProteinGroups.info()

loader = alphastats.loader.MaxQuantLoader( file="C:/Users/hekun/Downloads/proteinGroupsDemo.txt", intensity_column="LFQ intensity [sample]", # for indexing we are going to use the gene name columm # it is adivsed to use the ProteinIDs for indexing as these are unique index_column="Protein IDs", gene_names_column=None, ) ds = DataSet( loader=loader, metadata_path_or_df="C:/Users/hekun/Downloads/metadataDemo.xlsx", sample_column="sample", )

ds.preprocess(subset=True)

Below functions that I used, the running time is like forever:

plot = ds.plot_sampledistribution(color = "disease") plot.show(renderer = "SVG")

plot = ds.plot_samplehistograms() plot.show(renderer = "svg", width=1000, height=1000) plot.write_image("samplehistograms.pdf")

Any thing wrong I am here? Thank you!

[mschwoer]

Hey, thanks for reaching out. Could you pinpoint which part is taking long, e.g. by separating the commands into several cells?

Also, you might try dropping the "renderer = "svg", part for testing.

best, Magnus