Mercurial > repos > ebi-gxa > decoupler_pathway_inference

annotate decoupler_pseudobulk.py @ 3:c6787c2aee46 draft

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
author ebi-gxa
date Mon, 15 Jul 2024 10:56:37 +0000
parents 77d680b36e23
children 6c30272fb587
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77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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1 import argparse
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3 import anndata
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4 import decoupler
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5 import pandas as pd
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6
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8 def get_pseudobulk(
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9 adata,
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10 sample_col,
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11 groups_col,
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12 layer=None,
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13 mode="sum",
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14 min_cells=10,
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15 min_counts=1000,
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16 use_raw=False,
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17 ):
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18 """
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19 >>> import scanpy as sc
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20 >>> adata = sc.datasets.pbmc68k_reduced()
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21 >>> adata.X = abs(adata.X).astype(int)
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22 >>> pseudobulk = get_pseudobulk(adata, "bulk_labels", "louvain")
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23 """
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25 return decoupler.get_pseudobulk(
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26 adata,
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27 sample_col=sample_col,
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28 groups_col=groups_col,
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29 layer=layer,
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30 mode=mode,
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31 use_raw=use_raw,
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32 min_cells=min_cells,
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33 min_counts=min_counts,
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34 )
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35
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36
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37 def prepend_c_to_index(index_value):
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38 if index_value and index_value[0].isdigit():
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39 return "C" + index_value
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40 return index_value
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41
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42
3
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43 def genes_to_ignore_per_contrast_field(
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44 count_matrix_df,
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45 samples_metadata,
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46 sample_metadata_col_contrasts,
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47 min_counts_per_sample=5,
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48 use_cpms=False,
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49 ):
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50 """
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51 # This function calculates the genes to ignore per contrast field
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52 # (e.g., bulk_labels, louvain).
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53 # It does this by first getting the count matrix for each group,
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54 # then identifying genes with a count below a specified threshold.
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55 # The genes to ignore are those that are present in more than a specified
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56 # number of groups.
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57
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58 >>> import pandas as pd
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59 >>> samples_metadata = pd.DataFrame({'sample':
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60 ... ['S1', 'S2', 'S3',
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61 ... 'S4', 'S5', 'S6'],
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62 ... 'contrast_field':
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63 ... ['A', 'A', 'A', 'B', 'B', 'B']})
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64 >>> count_matrix_df = pd.DataFrame(
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65 ... {'S1':
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66 ... [30, 1, 40, 50, 30],
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67 ... 'S2':
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68 ... [40, 2, 60, 50, 80],
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69 ... 'S3':
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70 ... [80, 1, 60, 50, 50],
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71 ... 'S4': [1, 50, 50, 50, 2],
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72 ... 'S5': [3, 40, 40, 40, 2],
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73 ... 'S6': [0, 50, 50, 50, 1]})
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74 >>> count_matrix_df.index = ['Gene1', 'Gene2', 'Gene3', 'Gene4', 'Gene5']
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75 >>> df = genes_to_ignore_per_contrast_field(count_matrix_df,
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76 ... samples_metadata, min_counts_per_sample=5,
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77 ... sample_metadata_col_contrasts='contrast_field')
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78 >>> df[df['contrast_field'] == 'A'].genes_to_ignore.tolist()[0]
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79 'Gene2'
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80 >>> df[df['contrast_field'] == 'B'].genes_to_ignore.tolist()[0]
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81 'Gene1'
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82 >>> df[df['contrast_field'] == 'B'].genes_to_ignore.tolist()[1]
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83 'Gene5'
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84 """
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85
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86 # Initialize a dictionary to store the genes to ignore per contrast field
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87 contrast_fields = []
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88 genes_to_ignore = []
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89
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90 # Iterate over the contrast fields
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91 for contrast_field in samples_metadata[
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92 sample_metadata_col_contrasts
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93 ].unique():
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94 # Get the count matrix for the current contrast field
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95 count_matrix_field = count_matrix_df.loc[
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96 :,
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97 (
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98 samples_metadata[sample_metadata_col_contrasts]
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99 == contrast_field
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100 ).tolist(),
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101 ]
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102
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103 # We derive min_counts from the number of samples with that
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104 # contrast_field value
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105 min_counts = count_matrix_field.shape[1] * min_counts_per_sample
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106
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107 if use_cpms:
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108 # Convert counts to counts per million (CPM)
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109 count_matrix_field = (
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110 count_matrix_field.div(count_matrix_field.sum(axis=1), axis=0)
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111 * 1e6
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112 )
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113 min_counts = 1 # use 1 CPM
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114
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115 # Calculate the total number of cells in the current contrast field
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116 # (this produces a vector of counts per gene)
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117 total_counts_per_gene = count_matrix_field.sum(axis=1)
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118
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119 # Identify genes with a count below the specified threshold
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120 genes = total_counts_per_gene[
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121 total_counts_per_gene < min_counts
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122 ].index.tolist()
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123 if len(genes) > 0:
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124 # genes_to_ignore[contrast_field] = " ".join(genes)
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125 for gene in genes:
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126 genes_to_ignore.append(gene)
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127 contrast_fields.append(contrast_field)
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128 # transform gene_to_ignore to a DataFrame
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129 # genes_to_ignore_df = pd.DataFrame(genes_to_ignore.items(),
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130 # columns=["contrast_field", "genes_to_ignore"])
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131 genes_to_ignore_df = pd.DataFrame(
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132 {"contrast_field": contrast_fields, "genes_to_ignore": genes_to_ignore}
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133 )
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134 return genes_to_ignore_df
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135
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136
0
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137 # write results for loading into DESeq2
3
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138 def write_DESeq2_inputs(
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139 pdata,
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140 layer=None,
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141 output_dir="",
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142 factor_fields=None,
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143 min_counts_per_sample_marking=20,
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144 ):
0
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145 """
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146 >>> import scanpy as sc
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147 >>> adata = sc.datasets.pbmc68k_reduced()
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148 >>> adata.X = abs(adata.X).astype(int)
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149 >>> pseudobulk = get_pseudobulk(adata, "bulk_labels", "louvain")
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150 >>> write_DESeq2_inputs(pseudobulk)
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151 """
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152 # add / to output_dir if is not empty or if it doesn't end with /
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153 if output_dir != "" and not output_dir.endswith("/"):
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154 output_dir = output_dir + "/"
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155 obs_for_deseq = pdata.obs.copy()
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156 # replace any index starting with digits to start with C instead.
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157 obs_for_deseq.rename(index=prepend_c_to_index, inplace=True)
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158 # avoid dash that is read as point on R colnames.
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159 obs_for_deseq.index = obs_for_deseq.index.str.replace("-", "_")
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160 obs_for_deseq.index = obs_for_deseq.index.str.replace(" ", "_")
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161 col_metadata_file = f"{output_dir}col_metadata.tsv"
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162 # write obs to a col_metadata file
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163 if factor_fields:
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164 # only output the index plus the columns in factor_fields in that order
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165 obs_for_deseq[factor_fields].to_csv(
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166 col_metadata_file, sep="\t", index=True
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167 )
0
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168 else:
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169 obs_for_deseq.to_csv(col_metadata_file, sep="\t", index=True)
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170 # write var to a gene_metadata file
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171 pdata.var.to_csv(f"{output_dir}gene_metadata.tsv", sep="\t", index=True)
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172 # write the counts matrix of a specified layer to file
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173 if layer is None:
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174 # write the X numpy matrix transposed to file
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175 df = pd.DataFrame(
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176 pdata.X.T, index=pdata.var.index, columns=obs_for_deseq.index
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177 )
0
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178 else:
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179 df = pd.DataFrame(
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180 pdata.layers[layer].T,
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181 index=pdata.var.index,
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182 columns=obs_for_deseq.index,
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183 )
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184 df.to_csv(f"{output_dir}counts_matrix.tsv", sep="\t", index_label="")
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185
3
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186 if factor_fields:
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187 df_genes_ignore = genes_to_ignore_per_contrast_field(
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188 count_matrix_df=df,
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189 samples_metadata=obs_for_deseq,
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190 sample_metadata_col_contrasts=factor_fields[0],
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191 min_counts_per_sample=min_counts_per_sample_marking,
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192 )
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193 df_genes_ignore.to_csv(
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194 f"{output_dir}genes_to_ignore_per_contrast_field.tsv", sep="\t"
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195 )
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196
0
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197
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198 def plot_pseudobulk_samples(
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199 pseudobulk_data,
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200 groupby,
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201 figsize=(10, 10),
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202 save_path=None,
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203 ):
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204 """
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205 >>> import scanpy as sc
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206 >>> adata = sc.datasets.pbmc68k_reduced()
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207 >>> adata.X = abs(adata.X).astype(int)
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208 >>> pseudobulk = get_pseudobulk(adata, "bulk_labels", "louvain")
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209 >>> plot_pseudobulk_samples(pseudobulk,
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210 ... groupby=["bulk_labels", "louvain"],
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211 ... figsize=(10, 10))
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212 """
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213 fig = decoupler.plot_psbulk_samples(
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214 pseudobulk_data, groupby=groupby, figsize=figsize, return_fig=True
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215 )
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216 if save_path:
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217 fig.savefig(f"{save_path}/pseudobulk_samples.png")
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218 else:
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219 fig.show()
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220
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221
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222 def plot_filter_by_expr(
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223 pseudobulk_data,
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224 group,
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225 min_count=None,
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226 min_total_count=None,
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227 save_path=None,
0
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228 ):
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229 """
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230 >>> import scanpy as sc
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231 >>> adata = sc.datasets.pbmc68k_reduced()
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232 >>> adata.X = abs(adata.X).astype(int)
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233 >>> pseudobulk = get_pseudobulk(adata, "bulk_labels", "louvain")
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234 >>> plot_filter_by_expr(pseudobulk, group="bulk_labels",
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235 ... min_count=10, min_total_count=200)
0
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236 """
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237 fig = decoupler.plot_filter_by_expr(
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238 pseudobulk_data,
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239 group=group,
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240 min_count=min_count,
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241 min_total_count=min_total_count,
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242 return_fig=True,
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243 )
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244 if save_path:
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245 fig.savefig(f"{save_path}/filter_by_expr.png")
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246 else:
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247 fig.show()
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248
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249
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250 def filter_by_expr(pdata, min_count=None, min_total_count=None):
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251 """
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252 >>> import scanpy as sc
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253 >>> adata = sc.datasets.pbmc68k_reduced()
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254 >>> adata.X = abs(adata.X).astype(int)
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255 >>> pseudobulk = get_pseudobulk(adata, "bulk_labels", "louvain")
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256 >>> pdata_filt = filter_by_expr(pseudobulk,
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257 ... min_count=10, min_total_count=200)
0
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258 """
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259 genes = decoupler.filter_by_expr(
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260 pdata, min_count=min_count, min_total_count=min_total_count
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261 )
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262 return pdata[:, genes].copy()
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263
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264
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265 def check_fields(fields, adata, obs=True, context=None):
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266 """
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267 >>> import scanpy as sc
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268 >>> adata = sc.datasets.pbmc68k_reduced()
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269 >>> check_fields(["bulk_labels", "louvain"], adata, obs=True)
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270 """
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271
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272 legend = ""
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273 if context:
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274 legend = f", passed in {context},"
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275 if obs:
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276 if not set(fields).issubset(set(adata.obs.columns)):
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277 raise ValueError(
3
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278 f"Some of the following fields {legend} are not present \
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279 in adata.obs: {fields}. \
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280 Possible fields are: {list(set(adata.obs.columns))}"
0
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281 )
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282 else:
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283 if not set(fields).issubset(set(adata.var.columns)):
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284 raise ValueError(
3
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285 f"Some of the following fields {legend} are not present \
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286 in adata.var: {fields}. \
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287 Possible fields are: {list(set(adata.var.columns))}"
0
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288 )
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289
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290
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291 def main(args):
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292 # Load AnnData object from file
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293 adata = anndata.read_h5ad(args.adata_file)
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294
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295 # Merge adata.obs fields specified in args.adata_obs_fields_to_merge
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296 if args.adata_obs_fields_to_merge:
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297 # first split potential groups by ":" and iterate over them
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298 for group in args.adata_obs_fields_to_merge.split(":"):
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299 fields = group.split(",")
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300 check_fields(fields, adata)
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301 adata = merge_adata_obs_fields(fields, adata)
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302
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303 check_fields([args.groupby, args.sample_key], adata)
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304
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305 factor_fields = None
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306 if args.factor_fields:
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307 factor_fields = args.factor_fields.split(",")
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308 check_fields(factor_fields, adata)
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309
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310 print(f"Using mode: {args.mode}")
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311 # Perform pseudobulk analysis
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312 pseudobulk_data = get_pseudobulk(
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313 adata,
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314 sample_col=args.sample_key,
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315 groups_col=args.groupby,
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316 layer=args.layer,
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317 mode=args.mode,
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318 use_raw=args.use_raw,
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319 min_cells=args.min_cells,
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320 min_counts=args.min_counts,
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321 )
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322
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323 # Plot pseudobulk samples
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324 plot_pseudobulk_samples(
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325 pseudobulk_data,
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326 args.groupby,
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327 save_path=args.save_path,
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328 figsize=args.plot_samples_figsize,
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329 )
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330
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331 plot_filter_by_expr(
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332 pseudobulk_data,
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333 group=args.groupby,
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334 min_count=args.min_counts,
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335 min_total_count=args.min_total_counts,
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336 save_path=args.save_path,
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337 )
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338
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339 # Filter by expression if enabled
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340 if args.filter_expr:
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341 filtered_adata = filter_by_expr(
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342 pseudobulk_data,
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343 min_count=args.min_counts,
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344 min_total_count=args.min_total_counts,
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345 )
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346
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347 pseudobulk_data = filtered_adata
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348
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349 # Save the pseudobulk data
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350 if args.anndata_output_path:
3
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351 pseudobulk_data.write_h5ad(
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352 args.anndata_output_path, compression="gzip"
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353 )
0
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354
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355 write_DESeq2_inputs(
3
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356 pseudobulk_data,
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357 output_dir=args.deseq2_output_path,
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358 factor_fields=factor_fields,
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359 min_counts_per_sample_marking=args.min_counts_per_sample_marking,
0
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360 )
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361
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362
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363 def merge_adata_obs_fields(obs_fields_to_merge, adata):
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364 """
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365 Merge adata.obs fields specified in args.adata_obs_fields_to_merge
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366
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367 Parameters
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368 ----------
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369 obs_fields_to_merge : str
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370 Fields in adata.obs to merge, comma separated
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371 adata : anndata.AnnData
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372 The AnnData object
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373
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374 Returns
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375 -------
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376 anndata.AnnData
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377 The merged AnnData object
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378
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379 docstring tests:
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380 >>> import scanpy as sc
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381 >>> ad = sc.datasets.pbmc68k_reduced()
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382 >>> ad = merge_adata_obs_fields(["bulk_labels","louvain"], ad)
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383 >>> ad.obs.columns
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384 Index(['bulk_labels', 'n_genes', 'percent_mito', 'n_counts', 'S_score',
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385 'G2M_score', 'phase', 'louvain', 'bulk_labels_louvain'],
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386 dtype='object')
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387 """
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388 field_name = "_".join(obs_fields_to_merge)
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389 for field in obs_fields_to_merge:
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390 if field not in adata.obs.columns:
3
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391 raise ValueError(
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392 f"The '{field}' column is not present in adata.obs."
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393 )
0
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394 if field_name not in adata.obs.columns:
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395 adata.obs[field_name] = adata.obs[field].astype(str)
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396 else:
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397 adata.obs[field_name] = (
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398 adata.obs[field_name] + "_" + adata.obs[field].astype(str)
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399 )
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400 return adata
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401
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402
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403 if __name__ == "__main__":
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404 # Create argument parser
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405 parser = argparse.ArgumentParser(
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406 description="Perform pseudobulk analysis on an AnnData object"
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407 )
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408
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409 # Add arguments
3
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410 parser.add_argument(
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411 "adata_file", type=str, help="Path to the AnnData file"
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412 )
0
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413 parser.add_argument(
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414 "-m",
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415 "--adata_obs_fields_to_merge",
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416 type=str,
3
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417 help="Fields in adata.obs to merge, comma separated. \
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418 You can have more than one set of fields, \
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419 separated by semi-colon ;",
0
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420 )
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421 parser.add_argument(
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422 "--groupby",
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423 type=str,
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424 required=True,
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425 help="The column in adata.obs that defines the groups",
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426 )
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427 parser.add_argument(
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428 "--sample_key",
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429 required=True,
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430 type=str,
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431 help="The column in adata.obs that defines the samples",
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diff changeset
432 )
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
433 # add argument for layer
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
434 parser.add_argument(
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
435 "--layer",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
436 type=str,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
437 default=None,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
438 help="The name of the layer of the AnnData object to use",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
439 )
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
440 # add argument for mode
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
441 parser.add_argument(
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
442 "--mode",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
443 type=str,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
444 default="sum",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
445 help="The mode for Decoupler pseudobulk analysis",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
446 choices=["sum", "mean", "median"],
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
447 )
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
448 # add boolean argument for use_raw
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
449 parser.add_argument(
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
450 "--use_raw",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
451 action="store_true",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
452 default=False,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
453 help="Whether to use the raw part of the AnnData object",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
454 )
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
455 # add argument for min_cells
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
456 parser.add_argument(
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
457 "--min_cells",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
458 type=int,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
459 default=10,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
460 help="Minimum number of cells for pseudobulk analysis",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
461 )
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
462 parser.add_argument(
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
463 "--save_path", type=str, help="Path to save the plot (optional)"
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
464 )
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
465 parser.add_argument(
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
466 "--min_counts",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
467 type=int,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
468 help="Minimum count threshold for filtering by expression",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
469 )
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
470 parser.add_argument(
3
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
parents: 0
diff changeset
471 "--min_counts_per_sample_marking",
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
parents: 0
diff changeset
472 type=int,
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
parents: 0
diff changeset
473 default=20,
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
parents: 0
diff changeset
474 help="Minimum count threshold per sample for \
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
parents: 0
diff changeset
475 marking genes to be ignored after DE",
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
parents: 0
diff changeset
476 )
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
parents: 0
diff changeset
477 parser.add_argument(
0
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
478 "--min_total_counts",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
479 type=int,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
480 help="Minimum total count threshold for filtering by expression",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
481 )
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
482 parser.add_argument(
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
483 "--anndata_output_path",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
484 type=str,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
485 help="Path to save the filtered AnnData object or pseudobulk data",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
486 )
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
487 parser.add_argument(
3
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
parents: 0
diff changeset
488 "--filter_expr",
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
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diff changeset
489 action="store_true",
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
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diff changeset
490 help="Enable filtering by expression",
0
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
491 )
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
492 parser.add_argument(
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
493 "--factor_fields",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
494 type=str,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
495 help="Comma separated list of fields for the factors",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
496 )
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
497 parser.add_argument(
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
498 "--deseq2_output_path",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
499 type=str,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
500 help="Path to save the DESeq2 inputs",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
501 required=True,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
502 )
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
503 parser.add_argument(
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
504 "--plot_samples_figsize",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
505 type=int,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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506 default=[10, 10],
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
507 nargs=2,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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508 help="Size of the samples plot as a tuple (two arguments)",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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509 )
3
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
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diff changeset
510 parser.add_argument(
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
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diff changeset
511 "--plot_filtering_figsize", type=int, default=[10, 10], nargs=2
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
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diff changeset
512 )
0
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
513
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
514 # Parse the command line arguments
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
515 args = parser.parse_args()
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
516
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
517 # Call the main function
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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518 main(args)