python/cell_cycle_gating/process_brdu_ph3.py
def plot_summary(dfm, object_level_folder, filename='scatter.pdf'):
    """Makes summary scatter plot of BrdU pH3 and returns summary
    data file of fraction of cells in each phase based on gating

    Parameters
    ----------
    dfm : pandas dataframe
        table containing well level metadata. Minimun columns required is
        well, cell_line, agent, and concentration.
    object_level_folder : str
        path to folder containing object level text files.
    filename : Optional[str]
         Name of .pdf file containing the summary plots per well.
         Default is scatter.pdf
    Returns
    -------
    dfs : pandas dataframe
        Summary of BrDu and pH3 based gating per well, and fraction of cells
        in each state.
    """
    dfm_ord = merge_metadata(dfm, object_level_folder)
    object_level_files = dfm_ord['object_level_file'].tolist()
    # object_level_files = [s for s in os.listdir(object_level_folder)
    #                       if 'Nuclei Selected[0].txt' in s]

    dfc = get_gates_per_well(dfm, object_level_folder, object_level_files)
    dfs = plot_scatter(dfc, dfm, object_level_folder,
                       object_level_files, filename)
    return dfs
Makes summary scatter plot of BrdU pH3 and returns summary
    data file of fraction of cells in each phase based on gating

    Parameters
    ----------
    dfm : pandas dataframe
        table containing well level metadata. Minimun columns required is
        well, cell_line, agent, and concentration.
    object_level_folder : str
        path to folder containing object level text files.
    filename : Optional[str]
         Name of .pdf file containing the summary plots per well.
         Default is scatter.pdf
    Returns
    -------
    dfs : pandas dataframe
        Summary of BrDu and pH3 based gating per well, and fraction of cells
        in each state.
    
Makes summary scatter plot of BrdU pH3 and returns summary
data file of fraction of cells in each phase based on gating

Parameters

dfm : pandas dataframe
table containing well level metadata. Minimun columns required is
well, cell_line, agent, and concentration.
object_level_folder : str
path to folder containing object level text files.
filename : Optional[str]
Name of .pdf file containing the summary plots per well.

dfs : pandas dataframe
Summary of BrDu and pH3 based gating per well, and fraction of cells
in each state.
Makes summary scatter plot of BrdU pH3 and returns summary data file of fraction of cells in each phase based on gating Parameters dfm : pandas dataframe table containing well level metadata . Minimun columns required is well cell_line agent and concentration . object_level_folder : str path to folder containing object level text files . filename : Optional [ str ] Name of . pdf file containing the summary plots per well . dfs : pandas dataframe Summary of BrDu and pH3 based gating per well and fraction of cells in each state .
def plot_summary(dfm, object_level_folder, filename='scatter.pdf'):
    dfm_ord = merge_metadata(dfm, object_level_folder)
    object_level_files = dfm_ord['object_level_file'].tolist()
    dfc = get_gates_per_well(dfm, object_level_folder, object_level_files)
    dfs = plot_scatter(dfc, dfm, object_level_folder,
                       object_level_files, filename)
    return dfs
def plot_summary ( dfm , object_level_folder , filename = 'scatter.pdf' ) : dfm_ord = merge_metadata ( dfm , object_level_folder ) object_level_files = dfm_ord [ 'object_level_file' ] . tolist ( ) dfc = get_gates_per_well ( dfm , object_level_folder , object_level_files ) dfs = plot_scatter ( dfc , dfm , object_level_folder , object_level_files , filename ) return dfs
Makes summary scatter plot of BrdU pH3 and returns summary
data file of fraction of cells in each phase based on gating
Makes summary scatter plot of BrdU pH3 and returns summary data file of fraction of cells in each phase based on gating
"""Makes summary scatter plot of BrdU pH3 and returns summary
    data file of fraction of cells in each phase based on gating

    Parameters
    ----------
    dfm : pandas dataframe
        table containing well level metadata. Minimun columns required is
        well, cell_line, agent, and concentration.
    object_level_folder : str
        path to folder containing object level text files.
    filename : Optional[str]
         Name of .pdf file containing the summary plots per well.
         Default is scatter.pdf
    Returns
    -------
    dfs : pandas dataframe
        Summary of BrDu and pH3 based gating per well, and fraction of cells
        in each state.
    """ # object_level_files = [s for s in os.listdir(object_level_folder) #                       if 'Nuclei Selected[0].txt' in s]
dfm
object_level_folder
filename