Mercurial > repos > goeckslab > bayestme_select_markers_and_plot
changeset 0:152dc84840ca draft
planemo upload for repository https://github.com/goeckslab/tools-st/tree/main/tools/bayesTME commit 26edd05a863adac97cb54a9fb2ae5613ce95df50
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Dec 03 19:46:43 2025 +0000 @@ -0,0 +1,30 @@ +<macros> + <token name="@TOOL_VERSION@">0.0.1</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">22.01</token> + + <xml name="bayestme_requirements"> + <requirements> + <container type="docker">jeffquinnmsk/bayestme:0a7cde6acac2ffc34e8ad00b7fab75f869d80de2</container> + </requirements> + </xml> + + <xml name="citations"> + <citations> + <citation type="doi">10.1016/j.cels.2023.06.003</citation> + </citations> + </xml> + + <xml name="filter_genes_options" > + + <param argument="--n-top-by-standard-deviation" type="integer" optional="false" label="Use the top N genes with the highest spatial variance"/> + + <!-- Additional filtering options --> + <section name="additional_filtering_options" title="Additional Filtering Parameters" expanded="false"> + <param argument="--spot-threshold" optional="true" type="float" label="Filter genes appearing in greater than the provided threshold of tissue spots"/> + <param argument="--filter-ribosomal-genes" type="boolean" checked="false" label="Filter ribosomal genes (based on gene name regex)"/> + </section> + + </xml> + +</macros> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/select_markers_and_plot.xml Wed Dec 03 19:46:43 2025 +0000 @@ -0,0 +1,241 @@ +<tool id="bayestme_select_markers_and_plot" name="BayesTME: Plot Deconvolution" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>Plot Deconvolution Results (and Select Marker Genes) with BayesTME </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="bayestme_requirements"/> + <command detect_errors="aggressive"><![CDATA[ + + ## Select Marker Genes Step (Required Prior to Plot Deconvolution) + select_marker_genes + --adata '${adata}' + --adata-output 'dataset_deconvolved_marker_genes.h5ad' + --deconvolution-result '${deconvolution_result}' + --alpha '${select_markers.alpha}' + --n-marker-genes '${select_markers.n_marker_genes}' + --marker-gene-method '${select_markers.marker_gene_method}' + #if $verbose + -v + #end if + && + + mkdir -p marker_gene_tables && + mv *csv marker_gene_tables && + + ## Plot Deconvolution Step + mkdir -p plot_deconvolution_figures && + plot_deconvolution + --adata 'dataset_deconvolved_marker_genes.h5ad' + --output-dir plot_deconvolution_figures + #if $verbose + -v + #end if + #if str($cell_naming_method.cell_names) == 'manual': + --cell-type-names '${cell_type_names}' + #else + --expression-truth '${expression_truth}' + --reference-scrna-celltype-column '${reference_scrna_celltype_column}' + --reference-scrna-sample-column '${reference_scrna_sample_column}' + #end if + + ]]></command> + + <inputs> + + <!-- Required Deconvolved ST Data--> + <param argument="--adata" type="data" format="h5ad" label="Input file, AnnData in h5 format. Expected to be annotated with deconvolution results"/> + <param argument="--deconvolution-result" type="data" format="h5" label="Input file, DeconvolutionResult in h5 format"/> + + <!-- Select Marker Gene Arguments --> + <section name="select_markers" title="Select Marker Genes Arguments" expanded="false"> + <param argument="--n-marker-genes" type="integer" value="10" label="Maximum number of marker genes per cell type"/> + <param argument="--alpha" value="0.05" type="float" label="Alpha cutoff for choosing marker genes"/> + <param argument="--marker-gene-method" type="select" label="Method for choosing marker genes" > + <option value="BEST_AVAILABLE" selected="true">BEST_AVAILABLE</option> + <option value="TIGHT">TIGHT</option> + <option value="FALSE_DISCOVERY_RATE">FALSE_DISCOVERY_RATE</option> + </param> + </section> + + <!-- Plot Deconvolution Arguments --> + <conditional name="cell_naming_method"> + <param name="cell_names" type="select" label="Cell Type Names"> + <option value="manual" selected="true">Manually Provide Cell Type Names</option> + <option value="reference">Use Cell Type Names From Expression Reference</option> + </param> + <!-- Manual Cell Type Names --> + <when value="manual"> + <param argument="--cell-type-names" type="text" optional="false" label="A comma separated list of cell type names to use for plots. For example 'type 1, type 2, type 3'"/> + </when> + <!-- scRNA Reference Cell Type Names --> + <when value="reference"> + <param argument="--expression-truth" type="data" format="h5ad" optional="false" label="Matched scRNA data in h5ad format used for reference-based deconvolution step"/> + <param argument="--reference-scrna-celltype-column" type="text" optional="false" label="The name of the column with celltype id in the matched scRNA anndata"/> + <param argument="--reference-scrna-sample-column" type="text" optional="false" label="The name of the column with sample id in the matched scRNA anndata"/> + </when> + </conditional> + + <!-- Additonal Arguments --> + <param argument="--verbose" type="boolean" checked="false" label="Enable verbose logging"/> + + </inputs> + + <outputs> + + <!-- Select Marker Genes Outputs --> + <data name="adata_output" format="h5ad" label="BayesTME Select Marker Genes on ${on_string}: dataset_deconvolved_marker_genes.h5ad" from_work_dir="dataset_deconvolved_marker_genes.h5ad"/> + <collection name="marker_tables" type="list" label="BayesTME Select Marker Genes on ${on_string}: Marker Gene Tables"> + <discover_datasets pattern="__name_and_ext__" directory="marker_gene_tables" ext="csv" /> + </collection> + + <!-- Plot Deconvolution Outputs --> + <collection name="deconvolution_plots" type="list" label="BayesTME Plot Deconvolution on ${on_string}"> + <discover_datasets pattern="__name_and_ext__" directory="plot_deconvolution_figures" ext="pdf" /> + </collection> + + </outputs> + + <tests> + + <!-- Reference-free Test --> + <test> + + <!-- Select Marker Genes Inputs --> + <param name="adata" value="refFree_test_data/dataset_deconvolved.h5ad"/> + <param name="deconvolution_result" value="refFree_test_data/deconvolution_samples.h5"/> + <section name="select_markers"> + <param name="n_marker_genes" value="10"/> + <param name="alpha" value="0.05"/> + </section> + + <!-- Plot Deconvolution Inputs --> + <section name="cell_naming_method"> + <param name="cell_names" value="manual"/> + <param name="cell_type_names" value="celltype1,celltype2,celltype3"/> + </section> + + <!-- Select Marker Genes Outputs --> + <output name="adata_output" file="refFree_test_data/dataset_deconvolved_marker_genes.h5ad" compare="sim_size" delta="50000"> + <assert_contents> + <has_h5_keys keys="varm/bayestme_cell_type_marker"/> + </assert_contents> + </output> + <output_collection name="marker_tables" type="list" count="3"> + <element name="marker_genes" file="refFree_test_data/marker_genes.csv" compare="sim_size" delta="20000" ftype="csv"/> + <element name="omega" file="refFree_test_data/omega.csv" compare="sim_size" delta="20000" ftype="csv"/> + <element name="relative_expression" file="refFree_test_data/relative_expression.csv" compare="sim_size" delta="20000" ftype="csv"/> + </output_collection> + + <!-- Plot Deconvolution Outputs --> + <output_collection name="deconvolution_plots" type="list" count="9"> + <element name="cell_num_one_vs_all_scatterpie__celltype1" file="refFree_test_data/cell_num_one_vs_all_scatterpie__celltype1.pdf" compare="sim_size" delta="20000" ftype="pdf"/> + <element name="cell_num_one_vs_all_scatterpie__celltype2" file="refFree_test_data/cell_num_one_vs_all_scatterpie__celltype2.pdf" compare="sim_size" delta="20000" ftype="pdf"/> + <element name="cell_num_one_vs_all_scatterpie__celltype3" file="refFree_test_data/cell_num_one_vs_all_scatterpie__celltype3.pdf" compare="sim_size" delta="20000" ftype="pdf"/> + <element name="cell_num_scatterpie" file="refFree_test_data/cell_num_scatterpie.pdf" compare="sim_size" delta="20000" ftype="pdf"/> + <element name="cell_type_counts" file="refFree_test_data/cell_type_counts.pdf" compare="sim_size" delta="20000" ftype="pdf"/> + <element name="cell_type_probabilities" file="refFree_test_data/cell_type_probabilities.pdf" compare="sim_size" delta="20000" ftype="pdf"/> + <element name="marker_genes" file="refFree_test_data/marker_genes.pdf" compare="sim_size" delta="20000" ftype="pdf"/> + <element name="rank_genes_groups" file="refFree_test_data/rank_genes_groups.pdf" compare="sim_size" delta="20000" ftype="pdf"/> + <element name="rank_genes_groups_sharey" file="refFree_test_data/rank_genes_groups_sharey.pdf" compare="sim_size" delta="20000" ftype="pdf"/> + </output_collection> + </test> + + <!-- Reference-based Test --> + <test> + + <!-- Select Marker Genes Inputs --> + <param name="adata" value="refBased_test_data/dataset_deconvolved.h5ad"/> + <param name="deconvolution_result" value="refBased_test_data/deconvolution_samples.h5"/> + <section name="select_markers"> + <param name="n_marker_genes" value="10"/> + <param name="alpha" value="0.05"/> + </section> + + <!-- Plot Deconvolution Inputs --> + <section name="cell_naming_method"> + <param name="cell_names" value="reference"/> + <param name="expression_truth" value="refBased_test_data/scRef_test_dataset.h5ad"/> + <param name="reference_scrna_celltype_column" value="cell_type"/> + <param name="reference_scrna_sample_column" value="donor_id"/> + </section> + + <!-- Select Marker Genes Outputs --> + <output name="adata_output" file="refBased_test_data/dataset_deconvolved_marker_genes.h5ad" compare="sim_size" delta="50000"> + <assert_contents> + <has_h5_keys keys="varm/bayestme_cell_type_marker"/> + </assert_contents> + </output> + <output_collection name="marker_tables" type="list" count="3"> + <element name="marker_genes" file="refFree_test_data/marker_genes.csv" compare="sim_size" delta="20000" ftype="csv"/> + <element name="omega" file="refFree_test_data/omega.csv" compare="sim_size" delta="20000" ftype="csv"/> + <element name="relative_expression" file="refFree_test_data/relative_expression.csv" compare="sim_size" delta="20000" ftype="csv"/> + </output_collection> + + <!-- Plot Deconvolution Outputs --> + <output_collection name="deconvolution_plots" type="list" count="12"> + <element name="cell_num_one_vs_all_scatterpie__acinar cell" file="refBased_test_data/cell_num_one_vs_all_scatterpie__acinar_cell.pdf" compare="sim_size" delta="20000" ftype="pdf"/> + <element name="cell_num_one_vs_all_scatterpie__pancreatic ductal cell" file="refBased_test_data/cell_num_one_vs_all_scatterpie__pancreatic_ductal_cell.pdf" compare="sim_size" delta="20000" ftype="pdf"/> + <element name="cell_num_one_vs_all_scatterpie__type A enteroendocrine cell" file="refBased_test_data/cell_num_one_vs_all_scatterpie__type_A_enteroendocrine_cell.pdf" compare="sim_size" delta="20000" ftype="pdf"/> + <element name="cell_num_one_vs_all_scatterpie__type B pancreatic cell" file="refBased_test_data/cell_num_one_vs_all_scatterpie__type_B_pancreatic_cell.pdf" compare="sim_size" delta="20000" ftype="pdf"/> + <element name="cell_num_one_vs_all_scatterpie__type D enteroendocrine cell" file="refBased_test_data/cell_num_one_vs_all_scatterpie__type_D_enteroendocrine_cell.pdf" compare="sim_size" delta="20000" ftype="pdf"/> + <element name="cell_num_one_vs_all_scatterpie__unknown" file="refBased_test_data/cell_num_one_vs_all_scatterpie__unknown.pdf" compare="sim_size" delta="20000" ftype="pdf"/> + <element name="cell_num_scatterpie" file="refBased_test_data/cell_num_scatterpie.pdf" compare="sim_size" delta="20000" ftype="pdf"/> + <element name="cell_type_counts" file="refBased_test_data/cell_type_counts.pdf" compare="sim_size" delta="20000" ftype="pdf"/> + <element name="cell_type_probabilities" file="refBased_test_data/cell_type_probabilities.pdf" compare="sim_size" delta="20000" ftype="pdf"/> + <element name="marker_genes" file="refBased_test_data/marker_genes.pdf" compare="sim_size" delta="20000" ftype="pdf"/> + <element name="rank_genes_groups" file="refBased_test_data/rank_genes_groups.pdf" compare="sim_size" delta="20000" ftype="pdf"/> + <element name="rank_genes_groups_sharey" file="refBased_test_data/rank_genes_groups_sharey.pdf" compare="sim_size" delta="20000" ftype="pdf"/> + </output_collection> + </test> + + </tests> + + <help> + +<![CDATA[ + +usage: select_marker_genes [-h] [--adata ADATA] [--adata-output ADATA_OUTPUT] [-i] [--deconvolution-result DECONVOLUTION_RESULT] + [--n-marker-genes N_MARKER_GENES] [--alpha ALPHA] [--marker-gene-method TIGHT,BEST_AVAILABLE,FALSE_DISCOVERY_RATE] [-v] + +Perform marker gene selection + +options: + -h, --help show this help message and exit + --adata ADATA Input file, AnnData in h5 format + --adata-output ADATA_OUTPUT + A new AnnData in h5 format created with the deconvolution summary results appended. + -i, --inplace If provided, append deconvolution summary results to the --adata archive in place + --deconvolution-result DECONVOLUTION_RESULT + Input file, DeconvolutionResult in h5 format + --n-marker-genes N_MARKER_GENES + Maximum number of marker genes per cell type. + --alpha ALPHA Alpha cutoff for choosing marker genes. + --marker-gene-method TIGHT,BEST_AVAILABLE,FALSE_DISCOVERY_RATE + Method for choosing marker genes. + -v, --verbose Enable verbose logging + +usage: plot_deconvolution [-h] [--adata ADATA] [--output-dir OUTPUT_DIR] [--cell-type-names CELL_TYPE_NAMES] [--expression-truth EXPRESSION_TRUTH] + [--reference-scrna-celltype-column REFERENCE_SCRNA_CELLTYPE_COLUMN] + [--reference-scrna-sample-column REFERENCE_SCRNA_SAMPLE_COLUMN] [-v] + +Plot deconvolution results + +options: + -h, --help show this help message and exit + --adata ADATA Input file, AnnData in h5 format. Expected to be annotated with deconvolution results. + --output-dir OUTPUT_DIR + Output directory. + --cell-type-names CELL_TYPE_NAMES + A comma separated list of cell type names to use for plots.For example --cell-type-names "type 1, type 2, type 3" + --expression-truth EXPRESSION_TRUTH + Use expression ground truth from one or matched scRNA datasets. + --reference-scrna-celltype-column REFERENCE_SCRNA_CELLTYPE_COLUMN + The name of the column with celltype id in the matched scRNA anndata. + --reference-scrna-sample-column REFERENCE_SCRNA_SAMPLE_COLUMN + The name of the column with sample id in the matched scRNA anndata. + -v, --verbose Enable verbose logging + +]]> + </help> + <expand macro="citations"/> +</tool> \ No newline at end of file
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refBased_test_data/marker_genes.csv Wed Dec 03 19:46:43 2025 +0000 @@ -0,0 +1,241 @@ +gene_name,rank_in_cell_type,cell_type +BRI3,0,1 +SRSF3,1,1 +IFITM3,2,1 +LSM3,3,1 +MYL6,4,1 +AGR2,5,1 +CPNE3,6,1 +TOMM5,7,1 +SNRPG,8,1 +MORF4L2,9,1 +APOE,10,1 +TOMM7,11,1 +RAD21,12,1 +GFRA1,13,1 +WBP1,14,1 +CCT2,15,1 +NAA20,16,1 +NOP10,17,1 +DHX30,18,1 +HLA-DRA,19,1 +KRT10,20,1 +RARRES2,21,1 +SRSF5,22,1 +HMGA1,23,1 +MT2A,24,1 +POMP,25,1 +TKT,26,1 +TMED10,27,1 +TSTD1,28,1 +CNIH4,29,1 +PSMD2,30,1 +RABEP1,31,1 +APEX1,32,1 +TYROBP,33,1 +BANF1,34,1 +SNRPE,35,1 +ACADSB,36,1 +HSP90AB1,37,1 +PRDX3,38,1 +CSTB,39,1 +CNIH4,0,2 +ACADSB,1,2 +TKT,2,2 +HSP90AB1,3,2 +RAD21,4,2 +WBP1,5,2 +CCT2,6,2 +HMGA1,7,2 +BANF1,8,2 +HLA-DRA,9,2 +TSTD1,10,2 +PSMD2,11,2 +POMP,12,2 +BRI3,13,2 +MT2A,14,2 +MORF4L2,15,2 +TOMM7,16,2 +RARRES2,17,2 +SNRPG,18,2 +APEX1,19,2 +AGR2,20,2 +NAA20,21,2 +NOP10,22,2 +TMED10,23,2 +TOMM5,24,2 +KRT10,25,2 +DHX30,26,2 +TYROBP,27,2 +PRDX3,28,2 +SRSF3,29,2 +SNRPE,30,2 +IFITM3,31,2 +RABEP1,32,2 +GFRA1,33,2 +LSM3,34,2 +CPNE3,35,2 +APOE,36,2 +SRSF5,37,2 +MYL6,38,2 +CSTB,39,2 +MT2A,0,3 +WBP1,1,3 +CSTB,2,3 +SRSF5,3,3 +NOP10,4,3 +TMED10,5,3 +SRSF3,6,3 +DHX30,7,3 +MYL6,8,3 +TYROBP,9,3 +TSTD1,10,3 +APOE,11,3 +CCT2,12,3 +RAD21,13,3 +CPNE3,14,3 +NAA20,15,3 +LSM3,16,3 +ACADSB,17,3 +RARRES2,18,3 +RABEP1,19,3 +TOMM5,20,3 +SNRPE,21,3 +TKT,22,3 +IFITM3,23,3 +PRDX3,24,3 +HMGA1,25,3 +HLA-DRA,26,3 +POMP,27,3 +HSP90AB1,28,3 +KRT10,29,3 +TOMM7,30,3 +MORF4L2,31,3 +BANF1,32,3 +APEX1,33,3 +AGR2,34,3 +SNRPG,35,3 +GFRA1,36,3 +PSMD2,37,3 +CNIH4,38,3 +BRI3,39,3 +RABEP1,0,4 +PRDX3,1,4 +HSP90AB1,2,4 +SNRPE,3,4 +TYROBP,4,4 +SRSF5,5,4 +RAD21,6,4 +RARRES2,7,4 +POMP,8,4 +NAA20,9,4 +TKT,10,4 +MYL6,11,4 +CCT2,12,4 +GFRA1,13,4 +SRSF3,14,4 +ACADSB,15,4 +NOP10,16,4 +TOMM7,17,4 +BANF1,18,4 +HMGA1,19,4 +APEX1,20,4 +CSTB,21,4 +TMED10,22,4 +AGR2,23,4 +TSTD1,24,4 +HLA-DRA,25,4 +CNIH4,26,4 +TOMM5,27,4 +MORF4L2,28,4 +PSMD2,29,4 +KRT10,30,4 +IFITM3,31,4 +LSM3,32,4 +DHX30,33,4 +MT2A,34,4 +WBP1,35,4 +CPNE3,36,4 +SNRPG,37,4 +APOE,38,4 +BRI3,39,4 +APEX1,0,5 +CPNE3,1,5 +CNIH4,2,5 +CSTB,3,5 +BANF1,4,5 +HLA-DRA,5,5 +TOMM5,6,5 +MT2A,7,5 +MYL6,8,5 +KRT10,9,5 +SNRPE,10,5 +TMED10,11,5 +POMP,12,5 +AGR2,13,5 +MORF4L2,14,5 +LSM3,15,5 +PRDX3,16,5 +APOE,17,5 +HSP90AB1,18,5 +TYROBP,19,5 +HMGA1,20,5 +NOP10,21,5 +DHX30,22,5 +CCT2,23,5 +SRSF3,24,5 +SNRPG,25,5 +PSMD2,26,5 +TSTD1,27,5 +GFRA1,28,5 +RABEP1,29,5 +WBP1,30,5 +TOMM7,31,5 +IFITM3,32,5 +TKT,33,5 +NAA20,34,5 +ACADSB,35,5 +RAD21,36,5 +RARRES2,37,5 +BRI3,38,5 +SRSF5,39,5 +PSMD2,0,6 +GFRA1,1,6 +DHX30,2,6 +SNRPG,3,6 +KRT10,4,6 +IFITM3,5,6 +APOE,6,6 +SNRPE,7,6 +LSM3,8,6 +SRSF5,9,6 +AGR2,10,6 +ACADSB,11,6 +TKT,12,6 +RARRES2,13,6 +HLA-DRA,14,6 +HMGA1,15,6 +TYROBP,16,6 +PRDX3,17,6 +NAA20,18,6 +BRI3,19,6 +TOMM7,20,6 +TSTD1,21,6 +BANF1,22,6 +RABEP1,23,6 +POMP,24,6 +MORF4L2,25,6 +CPNE3,26,6 +APEX1,27,6 +TOMM5,28,6 +CSTB,29,6 +TMED10,30,6 +NOP10,31,6 +RAD21,32,6 +WBP1,33,6 +MYL6,34,6 +CCT2,35,6 +HSP90AB1,36,6 +SRSF3,37,6 +CNIH4,38,6 +MT2A,39,6
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refBased_test_data/omega.csv Wed Dec 03 19:46:43 2025 +0000 @@ -0,0 +1,41 @@ +,0,1,2,3,4,5 +AGR2,0.3,0.2,0.0,0.1,0.2,0.2 +MORF4L2,0.3,0.2,0.1,0.1,0.2,0.1 +SNRPE,0.0,0.1,0.1,0.3,0.2,0.3 +HSP90AB1,0.0,0.4,0.1,0.3,0.2,0.0 +GFRA1,0.2,0.1,0.0,0.2,0.1,0.4 +ACADSB,0.0,0.4,0.2,0.2,0.0,0.2 +APOE,0.2,0.0,0.2,0.0,0.2,0.4 +MT2A,0.1,0.3,0.4,0.0,0.2,0.0 +IFITM3,0.3,0.1,0.1,0.1,0.0,0.4 +KRT10,0.1,0.1,0.1,0.1,0.2,0.4 +HLA-DRA,0.1,0.3,0.1,0.1,0.2,0.2 +TSTD1,0.1,0.3,0.2,0.1,0.1,0.2 +CCT2,0.2,0.3,0.2,0.2,0.1,0.0 +WBP1,0.2,0.3,0.4,0.0,0.1,0.0 +TOMM5,0.3,0.2,0.1,0.1,0.2,0.1 +RAD21,0.2,0.3,0.2,0.3,0.0,0.0 +CNIH4,0.1,0.4,0.0,0.1,0.4,0.0 +TMED10,0.1,0.2,0.3,0.1,0.2,0.1 +TOMM7,0.2,0.2,0.1,0.2,0.1,0.2 +PRDX3,0.0,0.1,0.1,0.4,0.2,0.2 +LSM3,0.3,0.0,0.2,0.0,0.2,0.3 +NOP10,0.1,0.2,0.3,0.2,0.1,0.1 +HMGA1,0.1,0.3,0.1,0.2,0.1,0.2 +TYROBP,0.0,0.1,0.2,0.3,0.2,0.2 +RARRES2,0.1,0.2,0.2,0.3,0.0,0.2 +CSTB,0.0,0.0,0.4,0.2,0.3,0.1 +CPNE3,0.3,0.0,0.2,0.0,0.4,0.1 +BRI3,0.5,0.3,0.0,0.0,0.0,0.2 +SNRPG,0.3,0.2,0.0,0.0,0.1,0.4 +MYL6,0.3,0.0,0.3,0.2,0.2,0.0 +SRSF5,0.1,0.0,0.3,0.3,0.0,0.3 +POMP,0.1,0.3,0.1,0.2,0.2,0.1 +APEX1,0.1,0.2,0.0,0.2,0.4,0.1 +BANF1,0.0,0.3,0.1,0.2,0.3,0.1 +DHX30,0.1,0.1,0.3,0.0,0.1,0.4 +RABEP1,0.1,0.1,0.2,0.4,0.1,0.1 +SRSF3,0.3,0.1,0.3,0.2,0.1,0.0 +PSMD2,0.1,0.3,0.0,0.1,0.1,0.4 +NAA20,0.2,0.2,0.2,0.2,0.0,0.2 +TKT,0.1,0.4,0.1,0.2,0.0,0.2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refBased_test_data/relative_expression.csv Wed Dec 03 19:46:43 2025 +0000 @@ -0,0 +1,41 @@ +,0,1,2,3,4,5 +AGR2,-0.08380652219057083,-0.24061469733715057,-0.2815214991569519,-0.22048918902873993,-0.25506848096847534,0.08380652219057083 +MORF4L2,-0.23045410215854645,0.23045410215854645,-0.4615306854248047,-0.4566039443016052,-0.29516807198524475,-0.316114217042923 +SNRPE,-0.3119671046733856,-0.4708918631076813,-0.20415183901786804,-0.018912073224782944,-0.18750175833702087,0.018912073224782944 +HSP90AB1,-0.43157273530960083,-0.2963055372238159,-0.4264748990535736,0.2963055372238159,-0.4036998450756073,-0.5289340615272522 +GFRA1,-0.2077164351940155,-0.5465796589851379,-0.51600581407547,-0.11956971883773804,-0.42499789595603943,0.11956971883773804 +ACADSB,-0.4230344593524933,0.004193827509880066,-0.24471037089824677,-0.15493634343147278,-0.5466628074645996,-0.004193827509880066 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refFree_test_data/marker_genes.csv Wed Dec 03 19:46:43 2025 +0000 @@ -0,0 +1,121 @@ +gene_name,rank_in_cell_type,cell_type +S100A13,0,1 +GFRA1,1,1 +AGR2,2,1 +MORF4L2,3,1 +FN1,4,1 +HSBP1,5,1 +ENO1,6,1 +TTLL12,7,1 +LAPTM4B,8,1 +BST2,9,1 +KRT8,10,1 +NACA,11,1 +APOD,12,1 +HLA-DRA,13,1 +ARF1,14,1 +ACADSB,15,1 +SPP1,16,1 +CXCL14,17,1 +SNRPE,18,1 +IFITM3,19,1 +KRT19,20,1 +ATP5F1B,21,1 +S100P,22,1 +CTTN,23,1 +HSP90AB1,24,1 +BTF3,25,1 +TPI1,26,1 +SLC9A3R1,27,1 +PBX1,28,1 +APOE,29,1 +IDH2,30,1 +IER3,31,1 +TUBA1B,32,1 +MAGED2,33,1 +MT2A,34,1 +COX17,35,1 +TOMM6,36,1 +KRT10,37,1 +AGR3,38,1 +SELENOM,39,1 +SELENOM,0,2 +BTF3,1,2 +MAGED2,2,2 +S100P,3,2 +IFITM3,4,2 +COX17,5,2 +KRT10,6,2 +SLC9A3R1,7,2 +TPI1,8,2 +IER3,9,2 +ARF1,10,2 +TOMM6,11,2 +IDH2,12,2 +TUBA1B,13,2 +KRT8,14,2 +HLA-DRA,15,2 +BST2,16,2 +CXCL14,17,2 +KRT19,18,2 +APOE,19,2 +ENO1,20,2 +SPP1,21,2 +MORF4L2,22,2 +PBX1,23,2 +AGR2,24,2 +APOD,25,2 +ATP5F1B,26,2 +ACADSB,27,2 +NACA,28,2 +SNRPE,29,2 +HSBP1,30,2 +FN1,31,2 +AGR3,32,2 +LAPTM4B,33,2 +S100A13,34,2 +HSP90AB1,35,2 +GFRA1,36,2 +CTTN,37,2 +MT2A,38,2 +TTLL12,39,2 +AGR3,0,3 +MT2A,1,3 +TTLL12,2,3 +HSP90AB1,3,3 +CTTN,4,3 +PBX1,5,3 +APOE,6,3 +ATP5F1B,7,3 +LAPTM4B,8,3 +TOMM6,9,3 +KRT10,10,3 +SNRPE,11,3 +ACADSB,12,3 +TUBA1B,13,3 +NACA,14,3 +APOD,15,3 +IDH2,16,3 +HSBP1,17,3 +FN1,18,3 +IER3,19,3 +GFRA1,20,3 +SELENOM,21,3 +SPP1,22,3 +KRT19,23,3 +COX17,24,3 +S100A13,25,3 +CXCL14,26,3 +HLA-DRA,27,3 +ENO1,28,3 +MAGED2,29,3 +AGR2,30,3 +MORF4L2,31,3 +BST2,32,3 +SLC9A3R1,33,3 +KRT8,34,3 +TPI1,35,3 +S100P,36,3 +ARF1,37,3 +BTF3,38,3 +IFITM3,39,3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refFree_test_data/omega.csv Wed Dec 03 19:46:43 2025 +0000 @@ -0,0 +1,41 @@ +,0,1,2 +CXCL14,0.4,0.4,0.2 +AGR2,0.5,0.3,0.2 +KRT8,0.4,0.4,0.2 +MORF4L2,0.5,0.3,0.2 +IER3,0.2,0.5,0.3 +FN1,0.5,0.2,0.3 +S100A13,0.5,0.2,0.3 +SNRPE,0.3,0.3,0.4 +HSBP1,0.5,0.2,0.3 +CTTN,0.3,0.2,0.5 +S100P,0.3,0.6,0.1 +TUBA1B,0.2,0.5,0.3 +PBX1,0.2,0.3,0.5 +ARF1,0.4,0.5,0.1 +HSP90AB1,0.3,0.2,0.5 +GFRA1,0.5,0.2,0.3 +SLC9A3R1,0.3,0.5,0.2 +ACADSB,0.4,0.3,0.3 +APOE,0.2,0.4,0.4 +MAGED2,0.2,0.6,0.2 +ATP5F1B,0.3,0.3,0.4 +TTLL12,0.4,0.0,0.6 +KRT19,0.3,0.4,0.3 +MT2A,0.2,0.2,0.6 +IFITM3,0.3,0.6,0.1 +BST2,0.4,0.4,0.2 +ENO1,0.4,0.4,0.2 +TPI1,0.3,0.5,0.2 +SPP1,0.4,0.3,0.3 +SELENOM,0.0,0.7,0.3 +AGR3,0.1,0.2,0.7 +LAPTM4B,0.4,0.2,0.4 +NACA,0.4,0.3,0.3 +IDH2,0.2,0.5,0.3 +BTF3,0.3,0.6,0.1 +TOMM6,0.1,0.5,0.4 +KRT10,0.1,0.5,0.4 +HLA-DRA,0.4,0.4,0.2 +COX17,0.2,0.5,0.3 +APOD,0.4,0.3,0.3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refFree_test_data/relative_expression.csv Wed Dec 03 19:46:43 2025 +0000 @@ -0,0 +1,41 @@ +,0,1,2 +CXCL14,-0.4375229477882385,-0.16171614825725555,0.16171614825725555 +AGR2,0.17474493384361267,-0.17474493384361267,-0.25233936309814453 +KRT8,-0.17429867386817932,0.17429867386817932,-0.5132394433021545 +MORF4L2,0.13628606498241425,-0.13628606498241425,-0.2668810486793518 +IER3,-0.37387657165527344,0.3328932821750641,-0.3328932821750641 +FN1,0.1353853940963745,-0.37078720331192017,-0.1353853940963745 +S100A13,0.46118298172950745,-0.46118298172950745,-0.5808185338973999 +SNRPE,0.4548073410987854,-0.6118611693382263,-0.4548073410987854 +HSBP1,0.0903487578034401,-0.23363488912582397,-0.0903487578034401 +CTTN,-0.2016545981168747,-0.6537009477615356,0.2016545981168747 +S100P,-0.17843392491340637,0.1432689130306244,-0.1432689130306244 +TUBA1B,-0.4132199287414551,-0.21157126128673553,0.21157126128673553 +PBX1,0.11901863664388657,-0.13771884143352509,-0.11901863664388657 +ARF1,-0.3169371485710144,0.3169371485710144,-0.422046959400177 +HSP90AB1,-0.26272037625312805,-0.4617912769317627,0.26272037625312805 +GFRA1,0.3331877291202545,-0.4742777347564697,-0.3331877291202545 +SLC9A3R1,-0.3606945276260376,0.3606945276260376,-0.40291425585746765 +ACADSB,-0.36930787563323975,-0.44669845700263977,0.36930787563323975 +APOE,-0.18534696102142334,-0.33504199981689453,0.18534696102142334 +MAGED2,-0.47810444235801697,0.2290552854537964,-0.2290552854537964 +ATP5F1B,-0.03063628077507019,-0.29607343673706055,0.03063628077507019 +TTLL12,0.14046917855739594,-0.708142876625061,-0.14046917855739594 +KRT19,0.18354931473731995,-0.18354931473731995,-0.47579142451286316 +MT2A,-0.5393160581588745,-0.6572124361991882,0.5393160581588745 +IFITM3,0.19224987924098969,-0.19224987924098969,-0.6451092958450317 +BST2,-0.1251307874917984,0.1251307874917984,-0.3095334470272064 +ENO1,0.17155671119689941,-0.40797799825668335,-0.17155671119689941 +TPI1,-0.34889811277389526,0.34889811277389526,-0.5328922867774963 +SPP1,-0.3826879858970642,0.3826879858970642,-0.42629218101501465 +SELENOM,-0.5283265709877014,0.34312599897384644,-0.34312599897384644 +AGR3,-0.7603973150253296,-0.4380464553833008,0.4380464553833008 +LAPTM4B,-0.024069825187325478,-0.4395749866962433,0.024069825187325478 +NACA,-0.18196161091327667,-0.5017327666282654,0.18196161091327667 +IDH2,-0.33073437213897705,-0.07798266410827637,0.07798266410827637 +BTF3,-0.28069669008255005,0.28069669008255005,-0.5261001586914062 +TOMM6,-0.36111515760421753,0.12757104635238647,-0.12757104635238647 +KRT10,-0.46817606687545776,0.39888796210289,-0.39888796210289 +HLA-DRA,-0.2194845974445343,0.15029479563236237,-0.15029479563236237 +COX17,-0.549075722694397,0.47629469633102417,-0.47629469633102417 +APOD,-0.19722692668437958,-0.17616669833660126,0.17616669833660126