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Add fetcher for Gryglewski et al., 2018 expression maps

Open rmarkello opened this issue 5 years ago • 0 comments

The issue

There was a really nice paper last year by Gryglewski et al., 2018 that used some variogram modelling to generate "smooth" microarray expression maps for all the genes with valid Entrez IDs from the AHBA dataset. They've generously made these maps available online for download.

Proposed solution

I'm proposing a new function in abagen.datasets that lets people fetch maps for a given gene, provided they have the Entrez ID:

def fetch_gryglewski_map(entrez, data_dir=None, resume=True, verbose=1):
    """
    Fetches expression maps from [DS2]_ for gene with Entrez ID `entrez`

    Parameters
    ----------
    entrez : int
        Entrez ID of gene for which to fetch expression map
    data_dir : str, optional
        Directory where data should be downloaded and unpacked. Default:
        current directory
    resume : bool, optional
        Whether to resume download of a partly-downloaded file. Default: True
    verbose : int, optional
        Verbosity level (0 means no message). Default: 1

    Returns
    -------
    maps : dict
        Dictionary with keys ['vol', 'vol_mirror', 'surf', 'surf_mirror'],
        where corresponding values are lists of filepaths to downloaded Nifti
        (volumetric) and MGH (surface) files.

    References
    ----------
    .. [DS2] Gryglewski, G., Seiger, R., James, G. M., Godbersen, G. M.,
    Komorowski, A., Unterholzner, J., ... & Kasper, S. (2018). Spatial analysis
    and high resolution mapping of the human whole-brain transcriptome for
    integrative analysis in neuroimaging. NeuroImage, 176, 259-267.
    """

    # fetch and return dictionary with files for specified map
    # can use other abagen.datasets.fetch_X functions as models

rmarkello avatar Aug 30 '19 19:08 rmarkello