Merge pull request #7 from AmandaBirmingham/alt_norm_additions

Alternate normalization options
AmandaBirmingham · Jun 4, 2024 · 40b666c · 40b666c
2 parents 3e194c7 + 773b5c2
commit 40b666c
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Showing 6 changed files with 540 additions and 241 deletions.
diff --git a/docs/absolute_quant_example.xlsx b/docs/absolute_quant_example.xlsx
diff --git a/pysyndna/__init__.py b/pysyndna/__init__.py
@@ -3,7 +3,10 @@
     FIT_SYNDNA_MODELS_LOG_KEY
 from pysyndna.src.calc_cell_counts import calc_ogu_cell_counts_biom, \
     calc_ogu_cell_counts_per_g_of_sample_for_qiita, \
+    calc_ogu_cell_counts_per_cm2_of_sample_for_qiita, \
+    calc_ogu_cell_counts_per_ul_of_sample_for_qiita, \
     OGU_CELLS_PER_G_OF_GDNA_KEY, OGU_CELLS_PER_G_OF_SAMPLE_KEY, \
+    OGU_CELLS_PER_UL_OF_SAMPLE_KEY, OGU_CELLS_PER_CM2_OF_SAMPLE_KEY, \
     OGU_ID_KEY, OGU_LEN_IN_BP_KEY, OGU_PERCENT_COVERAGE_KEY, \
     CELL_COUNT_RESULT_KEY, CELL_COUNT_LOG_KEY
 from pysyndna.src.quant_orfs import \
@@ -17,13 +20,17 @@
            'fit_linear_regression_models_for_qiita',
            'calc_ogu_cell_counts_biom',
            'calc_ogu_cell_counts_per_g_of_sample_for_qiita',
+           'calc_ogu_cell_counts_per_cm2_of_sample_for_qiita',
+           'calc_ogu_cell_counts_per_ul_of_sample_for_qiita',
            'read_ogu_orf_coords_to_df',
            'validate_and_cast_ogu_orf_coords_df',
            'calc_copies_of_ogu_orf_ssrna_per_g_sample_from_dfs',
            'calc_copies_of_ogu_orf_ssrna_per_g_sample',
            'calc_copies_of_ogu_orf_ssrna_per_g_sample_for_qiita',
            'OGU_CELLS_PER_G_OF_GDNA_KEY',
            'OGU_CELLS_PER_G_OF_SAMPLE_KEY',
+           'OGU_CELLS_PER_UL_OF_SAMPLE_KEY',
+           'OGU_CELLS_PER_CM2_OF_SAMPLE_KEY',
            'SAMPLE_ID_KEY', 'OGU_ID_KEY', 'OGU_LEN_IN_BP_KEY',
            'OGU_ORF_ID_KEY', 'OGU_PERCENT_COVERAGE_KEY',
            'LIN_REGRESS_RESULT_KEY', 'FIT_SYNDNA_MODELS_LOG_KEY',