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Merge pull request #2 from lldelisle/dev2
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Release 1.1.1
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@lldelisle
lldelisle authored Oct 4, 2021
2 parents 4c472d3 + 1908786 commit 4ba358a
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Showing 31 changed files with 986 additions and 450 deletions.
1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -18,3 +18,4 @@ docs/savefig

# Big files
example/*.npz
docs/*.npz
2 changes: 1 addition & 1 deletion baredSC/_version.py
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@@ -1 +1 @@
__version__ = '1.1.0'
__version__ = '1.1.1'
16 changes: 10 additions & 6 deletions baredSC/baredSC_1d.py
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Expand Up @@ -143,7 +143,9 @@ def plot(oxpdf, x, logprob_values, samples, title, output, data, col_gene,
def parse_arguments(args=None):
argp = argparse.ArgumentParser(
description=("Run mcmc to get the pdf for a given gene using a"
" normal distributions."))
" normal distributions. The full documentation "
"is available at "
"https://baredsc.readthedocs.io"))
argprequired = argp.add_argument_group('Required arguments')
argpopt_data = argp.add_argument_group('Optional arguments to select input data')
argpopt_mcmc = argp.add_argument_group('Optional arguments to run MCMC')
Expand All @@ -152,7 +154,8 @@ def parse_arguments(args=None):
# Get data:
group = argprequired.add_mutually_exclusive_group(required=True)
group.add_argument('--input', default=None,
help="Input table with one line per cell"
help="Input table (tabular separated"
" with header) with one line per cell"
" columns with raw counts and one column"
" nCount_RNA with total number of UMI per cell"
" optionally other meta data to filter.")
Expand All @@ -163,15 +166,15 @@ def parse_arguments(args=None):
argpopt_data.add_argument('--metadata1ColName', default=None,
help="Name of the column with metadata1 to filter.")
argpopt_data.add_argument('--metadata1Values', default=None,
help="Comma separated values for metadata1.")
help="Comma separated values for metadata1 of cells to keep.")
argpopt_data.add_argument('--metadata2ColName', default=None,
help="Name of the column with metadata2 to filter.")
argpopt_data.add_argument('--metadata2Values', default=None,
help="Comma separated values for metadata2.")
help="Comma separated values for metadata2 of cells to keep.")
argpopt_data.add_argument('--metadata3ColName', default=None,
help="Name of the column with metadata3 to filter.")
argpopt_data.add_argument('--metadata3Values', default=None,
help="Comma separated values for metadata3.")
help="Comma separated values for metadata3 of cells to keep.")
# MCMC
argpopt_mcmc.add_argument('--xmin', default=0, type=float,
help="Minimum value to consider in x axis.")
Expand Down Expand Up @@ -212,7 +215,8 @@ def parse_arguments(args=None):
help="Change seed for another output.")
argpopt_mcmc.add_argument('--minNeff', default=None, type=float,
help="Will redo the MCMC with 10 times more samples until "
"Neff is greater that this value (Default is not set so will not rerun MCMC).")
"the number of effective samples that this value "
"(Default is not set so will not rerun MCMC).")
# To save/get MCMC
argpopt_mcmc.add_argument('--force', default=None, action='store_true',
help="Force to redo the mcmc even if output exists.")
Expand Down
16 changes: 10 additions & 6 deletions baredSC/baredSC_2d.py
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Original file line number Diff line number Diff line change
Expand Up @@ -231,7 +231,9 @@ def plot(oxpdf, oypdf, x, y, logprob_values, samples,
def parse_arguments(args=None):
argp = argparse.ArgumentParser(
description=("Run mcmc to get the pdf in 2D for 2 given genes using a"
" normal distributions."))
" normal distributions. The full documentation "
"is available at "
"https://baredsc.readthedocs.io"))
argprequired = argp.add_argument_group('Required arguments')
argpopt_data = argp.add_argument_group('Optional arguments to select input data')
argpopt_mcmc = argp.add_argument_group('Optional arguments to run MCMC')
Expand All @@ -240,7 +242,8 @@ def parse_arguments(args=None):
# To get the data
group = argprequired.add_mutually_exclusive_group(required=True)
group.add_argument('--input', default=None,
help="Input table with one line per cell"
help="Input table (tabular separated"
" with header) with one line per cell"
" columns with raw counts and one column"
" nCount_RNA with total number of UMI per cell"
" optionally other meta data to filter.")
Expand All @@ -253,15 +256,15 @@ def parse_arguments(args=None):
argpopt_data.add_argument('--metadata1ColName', default=None,
help="Name of the column with metadata1 to filter.")
argpopt_data.add_argument('--metadata1Values', default=None,
help="Comma separated values for metadata1.")
help="Comma separated values for metadata1 of cells to keep.")
argpopt_data.add_argument('--metadata2ColName', default=None,
help="Name of the column with metadata2 to filter.")
argpopt_data.add_argument('--metadata2Values', default=None,
help="Comma separated values for metadata2.")
help="Comma separated values for metadata2 of cells to keep.")
argpopt_data.add_argument('--metadata3ColName', default=None,
help="Name of the column with metadata3 to filter.")
argpopt_data.add_argument('--metadata3Values', default=None,
help="Comma separated values for metadata3.")
help="Comma separated values for metadata3 of cells to keep.")
# MCMC
argpopt_mcmc.add_argument('--xmin', default=0, type=float,
help="Minimum value to consider in x axis.")
Expand Down Expand Up @@ -323,7 +326,8 @@ def parse_arguments(args=None):
help="Change seed for another output.")
argpopt_mcmc.add_argument('--minNeff', default=None, type=float,
help="Will redo the MCMC with 10 times more samples until "
"Neff is greater that this value (Default is not set so will not rerun MCMC).")
"the number of effective samples that this value "
"(Default is not set so will not rerun MCMC).")
# To save/get MCMC
argpopt_mcmc.add_argument('--force', default=None, action='store_true',
help="Force to redo the mcmc even if output exists.")
Expand Down
9 changes: 5 additions & 4 deletions baredSC/combineMultipleModels_1d.py
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Original file line number Diff line number Diff line change
Expand Up @@ -88,7 +88,8 @@ def parse_arguments(args=None):
# Get data:
group = argprequired.add_mutually_exclusive_group(required=True)
group.add_argument('--input', default=None,
help="Input table with one line per cell"
help="Input table (tabular separated"
" with header) with one line per cell"
" columns with raw counts and one column"
" nCount_RNA with total number of UMI per cell"
" optionally other meta data to filter.")
Expand All @@ -99,15 +100,15 @@ def parse_arguments(args=None):
argpopt_data.add_argument('--metadata1ColName', default=None,
help="Name of the column with metadata1 to filter.")
argpopt_data.add_argument('--metadata1Values', default=None,
help="Comma separated values for metadata1.")
help="Comma separated values for metadata1 of cells to keep.")
argpopt_data.add_argument('--metadata2ColName', default=None,
help="Name of the column with metadata2 to filter.")
argpopt_data.add_argument('--metadata2Values', default=None,
help="Comma separated values for metadata2.")
help="Comma separated values for metadata2 of cells to keep.")
argpopt_data.add_argument('--metadata3ColName', default=None,
help="Name of the column with metadata3 to filter.")
argpopt_data.add_argument('--metadata3Values', default=None,
help="Comma separated values for metadata3.")
help="Comma separated values for metadata3 of cells to keep.")
# MCMC
argprequired.add_argument('--outputs', default=None, required=True, nargs='+',
help="Ouput files basename (will be npz)"
Expand Down
9 changes: 5 additions & 4 deletions baredSC/combineMultipleModels_2d.py
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Original file line number Diff line number Diff line change
Expand Up @@ -126,7 +126,8 @@ def parse_arguments(args=None):
# Get data:
group = argprequired.add_mutually_exclusive_group(required=True)
group.add_argument('--input', default=None,
help="Input table with one line per cell"
help="Input table (tabular separated"
" with header) with one line per cell"
" columns with raw counts and one column"
" nCount_RNA with total number of UMI per cell"
" optionally other meta data to filter.")
Expand All @@ -139,15 +140,15 @@ def parse_arguments(args=None):
argpopt_data.add_argument('--metadata1ColName', default=None,
help="Name of the column with metadata1 to filter.")
argpopt_data.add_argument('--metadata1Values', default=None,
help="Comma separated values for metadata1.")
help="Comma separated values for metadata1 of cells to keep.")
argpopt_data.add_argument('--metadata2ColName', default=None,
help="Name of the column with metadata2 to filter.")
argpopt_data.add_argument('--metadata2Values', default=None,
help="Comma separated values for metadata2.")
help="Comma separated values for metadata2 of cells to keep.")
argpopt_data.add_argument('--metadata3ColName', default=None,
help="Name of the column with metadata3 to filter.")
argpopt_data.add_argument('--metadata3Values', default=None,
help="Comma separated values for metadata3.")
help="Comma separated values for metadata3 of cells to keep.")
# MCMC
argprequired.add_argument('--outputs', default=None, required=True, nargs='+',
help="Ouput files basename (will be npz)"
Expand Down
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