| Previous changeset 13:48400c291093 (2024-04-23) |
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Commit message:
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9dbf2be568a0cea589fee8a42f070718d7966780-dirty |
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modified:
scmap_scmap_cell.xml |
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removed:
test-data/closest_cells.csv test-data/closest_cells_clusters.rds test-data/closest_cells_clusters.tsv test-data/closest_cells_similarities.csv test-data/index_cell.rds test-data/index_cluster.png test-data/index_cluster.rds test-data/project_cluster.csv test-data/project_cluster.tsv test-data/select_features.png test-data/select_features.rds test-data/test_sce.rds test-data/test_sce_processed.rds |
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| diff -r 48400c291093 -r 32ae4a600167 scmap_scmap_cell.xml --- a/scmap_scmap_cell.xml Tue Apr 23 07:48:26 2024 +0000 +++ b/scmap_scmap_cell.xml Mon Jul 08 08:53:18 2024 +0000 |
| [ |
| b'@@ -1,30 +1,30 @@\n-<tool id="scmap_scmap_cell" name="Scmap cell projection" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">\n+<tool id="scmap_scmap_cell" name="Scmap cell projection" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">\n <description>searches each cell in a query dataset for the nearest neighbours by cosine distance within a collection of reference datasets.</description>\n <macros>\n <import>scmap_macros.xml</import>\n </macros>\n <expand macro="requirements" />\n <command detect_errors="exit_code"><![CDATA[\n- scmap-scmap-cell.R \n- -i \'$index_single_cell_experiment\' \n- -p \'$project_single_cell_experiment\' \n- --number-nearest-neighbours \'$n_nearest_neighbours\' \n+ scmap-scmap-cell.R\n+ -i \'$index_single_cell_experiment\'\n+ -p \'$project_single_cell_experiment\'\n+ --number-nearest-neighbours \'$n_nearest_neighbours\'\n --nearest-neighbours-threshold \'$nearest_neighbours_threshold\'\n --threshold \'$threshold\'\n- --cluster-col \'${cluster_projection.cluster_col}\' \n- --output-object-file \'$output_single_cell_experiment\' \n- --closest-cells-text-file \'$closest_cells_text_file\' \n- --closest-cells-similarities-text-file \'$closest_cells_similarities_text_file\' \n+ --cluster-col \'${cluster_projection.cluster_col}\'\n+ --output-object-file \'$output_single_cell_experiment\'\n+ --closest-cells-text-file \'$closest_cells_text_file\'\n+ --closest-cells-similarities-text-file \'$closest_cells_similarities_text_file\'\n #if $cluster_projection\n- --output-clusters-text-file \'$closest_cells_clusters_csv\' \n- #end if \n+ --output-clusters-text-file \'$clusters_text_file\'\n+ #end if\n ]]></command>\n <inputs>\n <param type="data" name="index_single_cell_experiment" label="Index SingleCellExperiment object" format="rdata" help="File with serialized SingleCellExperiment object as produced by \'scmap select features\' and \'scmap index clusters\', onto which another dataset will be projected." />\n <param type="data" name="project_single_cell_experiment" label="SingleCellExperiment object to project" format="rdata" help="File with serialized SingleCellExperiment object to project onto the index\'" />\n <param name="n_nearest_neighbours" type="integer" label="Number of nearest neighbours" value=\'5\' help="A positive integer specifying the number of nearest neighbours to find" />\n <param name="nearest_neighbours_threshold" type="integer" label="Nearest neighbour threshold" value=\'3\' help="A positive integer specifying the number of matching nearest neighbours required to label a cell." />\n- <param name="threshold" type="integer" label="Similarity threshold" value=\'0.7\' help="Threshold on similarity (or probability for SVM and RF)." />\n+ <param name="threshold" type="float" label="Similarity threshold" value=\'0.7\' help="Threshold on similarity (or probability for SVM and RF)." />\n <conditional name="cluster_projection">\n <param name="do_cluster_projection" type="boolean" checked="false" label="Annotate cells of the projection dataset using labels of the reference?" help="If cell cluster annotation is available for the reference datasets, in addition to finding top 10 nearest neighbours scmap-cell also allows to annotate cells of the projection dataset using labels of the reference."/>\n <when value="true" >\n@@ -39,7 +39,7 @@\n <data name="output_single_cell_experiment" format="rdata" />\n <data name="closest_cells_text_file" format="tabular" />\n <data name="closest_cells_similarities_text_file" format="tabular" />\n- <data name="closest_cells_clusters_csv" format="tabular">\n+ <data name="clusters_text_file" format="tabular">\n <filter>cluster_projection[\'do_cluster_projection\']</filter>\n </data>\n'..b' <has_text_matching expression="Late.blastocyst..3..Cell.8.RPKM.\\tblast\\t0\\.938.*\\tblast"/>\n+ </assert_contents>\n+ </output>\n+ <output name="closest_cells_text_file" file="closest_cells.tsv"/>\n+ <output name="closest_cells_similarities_text_file">\n+ <assert_contents>\n+ <has_n_lines n="6"/>\n+ <has_text_matching expression="1\\t0\\.974.*\\t0\\.974.*\\t0\\.726.*\\t0\\.922.*\\t0\\.909.*"/>\n+ <has_text_matching expression="2\\t0\\.974.*\\t0\\.973.*\\t0\\.726.*\\t0\\.922.*\\t0\\.938.*"/>\n+ <has_text_matching expression="3\\t0\\.974.*\\t0\\.973.*\\t0\\.724.*\\t0\\.911.*\\t0\\.903.*"/>\n+ <has_text_matching expression="4\\t0\\.969.*\\t0\\.968.*\\t0\\.768.*\\t0\\.947.*\\t0\\.919.*"/>\n+ <has_text_matching expression="5\\t0\\.969.*\\t0\\.968.*\\t0\\.769.*\\t0\\.925.*\\t0\\.917.*"/>\n+ </assert_contents>\n+ </output>\n </test>\n <test>\n <param name="index_single_cell_experiment" value="index_cell.rds" ftype="rdata"/>\n@@ -63,17 +83,37 @@\n <param name="do_cluster_projection" value="true" />\n <param name="cluster_col" value="cell_type1" />\n </conditional>\n- <param name="nearest_neighbours_threshold" value="3" />\n- <param name="threshold" value="0.5" />\n- <output name="output_single_cell_experiment" file="closest_cells_clusters_copy.rds" compare="sim_size"/>\n- <output name="closest_cells_clusters_csv" file="closest_cells_clusters_copy.tsv" compare="sim_size" />\n- <output name="closest_cells_text_file" file="closest_cells_copy.tsv" compare="sim_size"/>\n- <output name="closest_cells_similarities_text_file" file="closest_cells_similarities_copy.tsv" compare="sim_size"/>\n+ <param name="nearest_neighbours_threshold" value="1" />\n+ <param name="threshold" value="0.2" />\n+ <output name="output_single_cell_experiment" file="closest_cells_clusters.rds" compare="sim_size"/>\n+ <output name="clusters_text_file">\n+ <assert_contents>\n+ <has_n_lines n="91" delta="1"/>\n+ <has_text_matching expression="Oocyte..1.RPKM.\\tzygote\\t0\\.974.*\\tzygote"/>\n+ <has_text_matching expression="Zygote..3.RPKM.\\tzygote\\t0\\.980.*\\tzygote"/>\n+ <has_text_matching expression="X2.cell.embryo.1..Cell.1.RPKM.\\t2cell\\t0\\.976.*\\t2cell"/>\n+ <has_text_matching expression="X4.cell.embryo.3..Cell.4.RPKM.\\t4cell\\t0\\.979.*\\t4cell"/>\n+ <has_text_matching expression="X8.cell.embryo.3..Cell.8.RPKM.\\t8cell\\t0\\.973.*\\t8cell"/>\n+ <has_text_matching expression="Morulae..2..Cell.8.RPKM.\\t16cell\\t0\\.967.*\\t16cell"/>\n+ <has_text_matching expression="Late.blastocyst..3..Cell.8.RPKM.\\tblast\\t0\\.938.*\\tblast"/>\n+ </assert_contents>\n+ </output>\n+ <output name="closest_cells_text_file" file="closest_cells.tsv"/>\n+ <output name="closest_cells_similarities_text_file">\n+ <assert_contents>\n+ <has_n_lines n="6"/>\n+ <has_text_matching expression="1\\t0\\.974.*\\t0\\.974.*\\t0\\.726.*\\t0\\.922.*\\t0\\.909.*"/>\n+ <has_text_matching expression="2\\t0\\.974.*\\t0\\.973.*\\t0\\.726.*\\t0\\.922.*\\t0\\.938.*"/>\n+ <has_text_matching expression="3\\t0\\.974.*\\t0\\.973.*\\t0\\.724.*\\t0\\.911.*\\t0\\.903.*"/>\n+ <has_text_matching expression="4\\t0\\.969.*\\t0\\.968.*\\t0\\.768.*\\t0\\.947.*\\t0\\.919.*"/>\n+ <has_text_matching expression="5\\t0\\.969.*\\t0\\.968.*\\t0\\.769.*\\t0\\.925.*\\t0\\.917.*"/>\n+ </assert_contents>\n+ </output>\n </test>\n </tests>\n <help><![CDATA[\n @HELP@\n- \n+\n @VERSION_HISTORY@\n ]]></help>\n <expand macro="citations" />\n' |
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| diff -r 48400c291093 -r 32ae4a600167 test-data/closest_cells.csv --- a/test-data/closest_cells.csv Tue Apr 23 07:48:26 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -,Oocyte..1.RPKM.,Oocyte..2.RPKM.,Oocyte..3.RPKM.,Zygote..1.RPKM.,Zygote..2.RPKM.,Zygote..3.RPKM.,X2.cell.embryo.1..Cell.1.RPKM.,X2.cell.embryo.1..Cell.2.RPKM.,X2.cell.embryo.2..Cell.1.RPKM.,X2.cell.embryo.2..Cell.2.RPKM.,X2.cell.embryo.3..Cell.1.RPKM.,X2.cell.embryo.3..Cell.2.RPKM.,X4.cell.embryo.1..Cell.1.RPKM.,X4.cell.embryo.1..Cell.2.RPKM.,X4.cell.embryo.1..Cell.3.RPKM.,X4.cell.embryo.1..Cell.4.RPKM.,X4.cell.embryo.2..Cell.1.RPKM.,X4.cell.embryo.2..Cell.2.RPKM.,X4.cell.embryo.2..Cell.3.RPKM.,X4.cell.embryo.2..Cell.4.RPKM.,X4.cell.embryo.3..Cell.1.RPKM.,X4.cell.embryo.3..Cell.2.RPKM.,X4.cell.embryo.3..Cell.3.RPKM.,X4.cell.embryo.3..Cell.4.RPKM.,X8.cell.embryo.1..Cell.1.RPKM.,X8.cell.embryo.1..Cell.2.RPKM.,X8.cell.embryo.1..Cell.3.RPKM.,X8.cell.embryo.1..Cell.4.RPKM.,X8.cell.embryo.2..Cell.1.RPKM.,X8.cell.embryo.2..Cell.2.RPKM.,X8.cell.embryo.2..Cell.3.RPKM.,X8.cell.embryo.2..Cell.4.RPKM.,X8.cell.embryo.2..Cell.5.RPKM.,X8.cell.embryo.2..Cell.6.RPKM.,X8.cell.embryo.2..Cell.7.RPKM.,X8.cell.embryo.2..Cell.8.RPKM.,X8.cell.embryo.3..Cell.1.RPKM.,X8.cell.embryo.3..Cell.2.RPKM.,X8.cell.embryo.3..Cell.3.RPKM.,X8.cell.embryo.3..Cell.4.RPKM.,X8.cell.embryo.3..Cell.5.RPKM.,X8.cell.embryo.3..Cell.6.RPKM.,X8.cell.embryo.3..Cell.7.RPKM.,X8.cell.embryo.3..Cell.8.RPKM.,Morulae..1..Cell.1.RPKM.,Morulae..1..Cell.2.RPKM.,Morulae..1..Cell.3.RPKM.,Morulae..1..Cell.4.RPKM.,Morulae..1..Cell.5.RPKM.,Morulae..1..Cell.6.RPKM.,Morulae..1..Cell.7.RPKM.,Morulae..1..Cell.8.RPKM.,Morulae..2..Cell.1.RPKM.,Morulae..2..Cell.2.RPKM.,Morulae..2..Cell.3.RPKM.,Morulae..2..Cell.4.RPKM.,Morulae..2..Cell.5.RPKM.,Morulae..2..Cell.6.RPKM.,Morulae..2..Cell.7.RPKM.,Morulae..2..Cell.8.RPKM.,Late.blastocyst..1..Cell.1.RPKM.,Late.blastocyst..1..Cell.2.RPKM.,Late.blastocyst..1..Cell.3.RPKM.,Late.blastocyst..1..Cell.4.RPKM.,Late.blastocyst..1..Cell.5.RPKM.,Late.blastocyst..1..Cell.6.RPKM.,Late.blastocyst..1..Cell.7.RPKM.,Late.blastocyst..1..Cell.8.RPKM.,Late.blastocyst..1..Cell.9.RPKM.,Late.blastocyst..1..Cell.10.RPKM.,Late.blastocyst..1..Cell.11.RPKM.,Late.blastocyst..1..Cell.12.RPKM.,Late.blastocyst..2..Cell.1.RPKM.,Late.blastocyst..2..Cell.2.RPKM.,Late.blastocyst..2..Cell.3.RPKM.,Late.blastocyst..2..Cell.4.RPKM.,Late.blastocyst..2..Cell.5.RPKM.,Late.blastocyst..2..Cell.6.RPKM.,Late.blastocyst..2..Cell.7.RPKM.,Late.blastocyst..2..Cell.8.RPKM.,Late.blastocyst..2..Cell.9.RPKM.,Late.blastocyst..2..Cell.10.RPKM.,Late.blastocyst..3..Cell.1.RPKM.,Late.blastocyst..3..Cell.2.RPKM.,Late.blastocyst..3..Cell.3.RPKM.,Late.blastocyst..3..Cell.4.RPKM.,Late.blastocyst..3..Cell.5.RPKM.,Late.blastocyst..3..Cell.6.RPKM.,Late.blastocyst..3..Cell.7.RPKM.,Late.blastocyst..3..Cell.8.RPKM. -1,1,1,1,6,6,6,10,10,10,10,12,10,23,19,24,22,14,13,24,13,21,24,23,24,28,27,27,25,34,35,36,32,34,34,35,30,37,42,44,38,38,37,39,39,48,49,47,49,46,49,49,27,57,54,55,55,54,51,55,54,62,67,67,63,71,67,62,66,69,69,71,78,65,87,84,78,78,81,82,82,78,81,88,84,90,75,83,78,88,88 -2,2,2,2,11,12,11,7,7,7,7,7,7,13,13,13,14,24,22,14,20,22,23,21,21,27,25,25,27,36,30,30,34,30,33,34,36,38,37,39,39,42,38,43,43,45,46,52,45,51,54,51,26,49,57,56,59,57,59,56,60,70,71,62,67,62,71,69,62,72,62,63,70,76,86,86,81,79,78,76,80,82,82,87,88,89,74,74,88,85,90 -3,3,3,3,12,10,12,8,8,8,8,8,11,14,24,23,21,19,16,19,23,23,18,22,22,26,26,26,26,30,36,34,36,33,36,36,35,40,40,40,41,40,40,38,44,49,54,26,51,54,51,50,28,51,50,59,60,53,58,58,53,61,61,63,64,69,66,64,82,70,70,72,81,71,75,75,76,81,76,78,76,81,78,75,80,88,86,86,90,77,81 -4,6,7,6,4,11,4,9,9,9,9,9,12,24,14,16,16,23,18,23,18,24,13,13,13,40,38,40,38,29,29,29,29,29,29,29,29,42,38,38,37,37,42,37,41,51,50,28,48,50,50,53,47,54,53,54,58,60,56,54,50,71,68,82,65,65,68,67,68,67,65,65,72,73,73,80,82,82,79,79,75,76,79,86,73,85,83,87,89,89,85 -5,5,5,5,5,5,5,12,12,12,12,11,5,22,23,15,24,17,21,17,22,18,22,24,23,25,28,28,28,31,31,31,35,36,35,31,31,41,41,41,40,41,41,41,38,53,51,27,50,49,46,46,52,53,51,58,56,51,55,59,51,65,62,71,72,70,72,66,78,65,72,69,65,70,74,74,79,77,82,77,84,72,76,83,75,72,87,75,85,90,89 |
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| diff -r 48400c291093 -r 32ae4a600167 test-data/closest_cells_clusters.rds |
| b |
| Binary file test-data/closest_cells_clusters.rds has changed |
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| diff -r 48400c291093 -r 32ae4a600167 test-data/closest_cells_clusters.tsv --- a/test-data/closest_cells_clusters.tsv Tue Apr 23 07:48:26 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,91 +0,0 @@ -cell scmap_cluster_labs scmap_cluster_siml combined_labs -Oocyte..1.RPKM. zygote 0.972457633278923 zygote -Oocyte..2.RPKM. zygote 0.972353568313767 zygote -Oocyte..3.RPKM. zygote 0.973371064673993 zygote -Zygote..1.RPKM. zygote 0.97866272698663 zygote -Zygote..2.RPKM. zygote 0.979717800854604 zygote -Zygote..3.RPKM. zygote 0.97984002400711 zygote -X2.cell.embryo.1..Cell.1.RPKM. 2cell 0.975860542596827 2cell -X2.cell.embryo.1..Cell.2.RPKM. 2cell 0.975977483944058 2cell -X2.cell.embryo.2..Cell.1.RPKM. 2cell 0.97534563242085 2cell -X2.cell.embryo.2..Cell.2.RPKM. 2cell 0.976532855604968 2cell -X2.cell.embryo.3..Cell.1.RPKM. 2cell 0.975715675528499 2cell -X2.cell.embryo.3..Cell.2.RPKM. 2cell 0.976512040050606 2cell -X4.cell.embryo.1..Cell.1.RPKM. 4cell 0.976740874886324 4cell -X4.cell.embryo.1..Cell.2.RPKM. 4cell 0.970679786566831 4cell -X4.cell.embryo.1..Cell.3.RPKM. 4cell 0.971937340916803 4cell -X4.cell.embryo.1..Cell.4.RPKM. 4cell 0.974396302382197 4cell -X4.cell.embryo.2..Cell.1.RPKM. 4cell 0.968256593061058 4cell -X4.cell.embryo.2..Cell.2.RPKM. 4cell 0.976000962530563 4cell -X4.cell.embryo.2..Cell.3.RPKM. 4cell 0.974456795916042 4cell -X4.cell.embryo.2..Cell.4.RPKM. 4cell 0.975046287156331 4cell -X4.cell.embryo.3..Cell.1.RPKM. 4cell 0.980907467386254 4cell -X4.cell.embryo.3..Cell.2.RPKM. 4cell 0.979702774175472 4cell -X4.cell.embryo.3..Cell.3.RPKM. 4cell 0.979541752074044 4cell -X4.cell.embryo.3..Cell.4.RPKM. 4cell 0.979397781619405 4cell -X8.cell.embryo.1..Cell.1.RPKM. 8cell 0.965866705260469 8cell -X8.cell.embryo.1..Cell.2.RPKM. 8cell 0.971874515954174 8cell -X8.cell.embryo.1..Cell.3.RPKM. 8cell 0.970182782492083 8cell -X8.cell.embryo.1..Cell.4.RPKM. 8cell 0.971803309754166 8cell -X8.cell.embryo.2..Cell.1.RPKM. 8cell 0.975660495961879 8cell -X8.cell.embryo.2..Cell.2.RPKM. 8cell 0.978697234565528 8cell -X8.cell.embryo.2..Cell.3.RPKM. 8cell 0.980500043303112 8cell -X8.cell.embryo.2..Cell.4.RPKM. 8cell 0.973337322820485 8cell -X8.cell.embryo.2..Cell.5.RPKM. 8cell 0.97050828475866 8cell -X8.cell.embryo.2..Cell.6.RPKM. 8cell 0.97427362884691 8cell -X8.cell.embryo.2..Cell.7.RPKM. 8cell 0.977362207861906 8cell -X8.cell.embryo.2..Cell.8.RPKM. 8cell 0.978677072589576 8cell -X8.cell.embryo.3..Cell.1.RPKM. 8cell 0.97989418833849 8cell -X8.cell.embryo.3..Cell.2.RPKM. 8cell 0.97485334405104 8cell -X8.cell.embryo.3..Cell.3.RPKM. 8cell 0.975859793936309 8cell -X8.cell.embryo.3..Cell.4.RPKM. 8cell 0.981490977097 8cell -X8.cell.embryo.3..Cell.5.RPKM. 8cell 0.981029618769028 8cell -X8.cell.embryo.3..Cell.6.RPKM. 8cell 0.969682040359692 8cell -X8.cell.embryo.3..Cell.7.RPKM. 8cell 0.978148246228053 8cell -X8.cell.embryo.3..Cell.8.RPKM. 8cell 0.970328380893092 8cell -Morulae..1..Cell.1.RPKM. 16cell 0.959918851368306 16cell -Morulae..1..Cell.2.RPKM. 16cell 0.973499865778146 16cell -Morulae..1..Cell.3.RPKM. 16cell 0.905095452914499 16cell -Morulae..1..Cell.4.RPKM. 16cell 0.975565450656408 16cell -Morulae..1..Cell.5.RPKM. 16cell 0.972676900609201 16cell -Morulae..1..Cell.6.RPKM. 16cell 0.965520701954854 16cell -Morulae..1..Cell.7.RPKM. 16cell 0.974360238512134 16cell -Morulae..1..Cell.8.RPKM. 16cell 0.89292960975856 16cell -Morulae..2..Cell.1.RPKM. 16cell 0.973068555642167 16cell -Morulae..2..Cell.2.RPKM. 16cell 0.972782844321894 16cell -Morulae..2..Cell.3.RPKM. 16cell 0.964788103357924 16cell -Morulae..2..Cell.4.RPKM. 16cell 0.966128218632723 16cell -Morulae..2..Cell.5.RPKM. 16cell 0.959906305241092 16cell -Morulae..2..Cell.6.RPKM. 16cell 0.973292643125946 16cell -Morulae..2..Cell.7.RPKM. 16cell 0.972824053645381 16cell -Morulae..2..Cell.8.RPKM. 16cell 0.966191355651732 16cell -Late.blastocyst..1..Cell.1.RPKM. blast 0.954545456827362 blast -Late.blastocyst..1..Cell.2.RPKM. blast 0.959479973403999 blast -Late.blastocyst..1..Cell.3.RPKM. blast 0.95220936077016 blast -Late.blastocyst..1..Cell.4.RPKM. blast 0.950460474784597 blast -Late.blastocyst..1..Cell.5.RPKM. blast 0.952198095399196 blast -Late.blastocyst..1..Cell.6.RPKM. blast 0.947932383616434 blast -Late.blastocyst..1..Cell.7.RPKM. blast 0.953028259974652 blast -Late.blastocyst..1..Cell.8.RPKM. blast 0.955242273190534 blast -Late.blastocyst..1..Cell.9.RPKM. blast 0.945069684662869 blast -Late.blastocyst..1..Cell.10.RPKM. blast 0.948997282545248 blast -Late.blastocyst..1..Cell.11.RPKM. blast 0.957933181323242 blast -Late.blastocyst..1..Cell.12.RPKM. blast 0.956477894281845 blast -Late.blastocyst..2..Cell.1.RPKM. blast 0.951896178479488 blast -Late.blastocyst..2..Cell.2.RPKM. blast 0.931976810185073 blast -Late.blastocyst..2..Cell.3.RPKM. blast 0.935585386310024 blast -Late.blastocyst..2..Cell.4.RPKM. blast 0.955286040867509 blast -Late.blastocyst..2..Cell.5.RPKM. blast 0.947612540470952 blast -Late.blastocyst..2..Cell.6.RPKM. blast 0.956938141272494 blast -Late.blastocyst..2..Cell.7.RPKM. blast 0.95796374641168 blast -Late.blastocyst..2..Cell.8.RPKM. blast 0.928236097734115 blast -Late.blastocyst..2..Cell.9.RPKM. blast 0.948137126389516 blast -Late.blastocyst..2..Cell.10.RPKM. blast 0.955220996266827 blast -Late.blastocyst..3..Cell.1.RPKM. blast 0.897154517212312 blast -Late.blastocyst..3..Cell.2.RPKM. blast 0.916287566525039 blast -Late.blastocyst..3..Cell.3.RPKM. blast 0.949016031543691 blast -Late.blastocyst..3..Cell.4.RPKM. blast 0.915241215759076 blast -Late.blastocyst..3..Cell.5.RPKM. blast 0.924787897158703 blast -Late.blastocyst..3..Cell.6.RPKM. blast 0.943459425658745 blast -Late.blastocyst..3..Cell.7.RPKM. blast 0.949859434636659 blast -Late.blastocyst..3..Cell.8.RPKM. blast 0.946067646237195 blast |
| b |
| diff -r 48400c291093 -r 32ae4a600167 test-data/closest_cells_similarities.csv --- a/test-data/closest_cells_similarities.csv Tue Apr 23 07:48:26 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,6 +0,0 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|
| b |
| diff -r 48400c291093 -r 32ae4a600167 test-data/index_cell.rds |
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| Binary file test-data/index_cell.rds has changed |
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| diff -r 48400c291093 -r 32ae4a600167 test-data/index_cluster.png |
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| Binary file test-data/index_cluster.png has changed |
| b |
| diff -r 48400c291093 -r 32ae4a600167 test-data/index_cluster.rds |
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| Binary file test-data/index_cluster.rds has changed |
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| diff -r 48400c291093 -r 32ae4a600167 test-data/project_cluster.csv --- a/test-data/project_cluster.csv Tue Apr 23 07:48:26 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,91 +0,0 @@ -,cell,scmap_cluster_labs,scmap_cluster_siml,combined_labs -1,Oocyte..1.RPKM.,zygote,0.994760865096957,zygote -2,Oocyte..2.RPKM.,zygote,0.995125744257364,zygote -3,Oocyte..3.RPKM.,zygote,0.995591648577841,zygote -4,Zygote..1.RPKM.,2cell,0.993401179090721,2cell -5,Zygote..2.RPKM.,2cell,0.995369354590786,2cell -6,Zygote..3.RPKM.,2cell,0.98710411159295,2cell -7,X2.cell.embryo.1..Cell.1.RPKM.,2cell,0.998499099285601,2cell -8,X2.cell.embryo.1..Cell.2.RPKM.,2cell,0.998846842740487,2cell -9,X2.cell.embryo.2..Cell.1.RPKM.,2cell,0.998606947244777,2cell -10,X2.cell.embryo.2..Cell.2.RPKM.,2cell,0.998676368789508,2cell -11,X2.cell.embryo.3..Cell.1.RPKM.,2cell,0.997663075228921,2cell -12,X2.cell.embryo.3..Cell.2.RPKM.,2cell,0.99770244480819,2cell -13,X4.cell.embryo.1..Cell.1.RPKM.,4cell,0.990134433448036,4cell -14,X4.cell.embryo.1..Cell.2.RPKM.,4cell,0.983906001584324,4cell -15,X4.cell.embryo.1..Cell.3.RPKM.,4cell,0.983025466176017,4cell 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| b |
| diff -r 48400c291093 -r 32ae4a600167 test-data/project_cluster.tsv --- a/test-data/project_cluster.tsv Tue Apr 23 07:48:26 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,91 +0,0 @@ -cell scmap_cluster_labs scmap_cluster_siml combined_labs -1 Oocyte..1.RPKM. zygote 0.994760865096957 zygote -2 Oocyte..2.RPKM. zygote 0.995125744257364 zygote -3 Oocyte..3.RPKM. zygote 0.995591648577841 zygote -4 Zygote..1.RPKM. 2cell 0.993401179090721 2cell -5 Zygote..2.RPKM. 2cell 0.995369354590786 2cell -6 Zygote..3.RPKM. 2cell 0.98710411159295 2cell -7 X2.cell.embryo.1..Cell.1.RPKM. 2cell 0.998499099285601 2cell -8 X2.cell.embryo.1..Cell.2.RPKM. 2cell 0.998846842740487 2cell -9 X2.cell.embryo.2..Cell.1.RPKM. 2cell 0.998606947244777 2cell -10 X2.cell.embryo.2..Cell.2.RPKM. 2cell 0.998676368789508 2cell -11 X2.cell.embryo.3..Cell.1.RPKM. 2cell 0.997663075228921 2cell -12 X2.cell.embryo.3..Cell.2.RPKM. 2cell 0.99770244480819 2cell -13 X4.cell.embryo.1..Cell.1.RPKM. 4cell 0.990134433448036 4cell -14 X4.cell.embryo.1..Cell.2.RPKM. 4cell 0.983906001584324 4cell -15 X4.cell.embryo.1..Cell.3.RPKM. 4cell 0.983025466176017 4cell -16 X4.cell.embryo.1..Cell.4.RPKM. 4cell 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Morulae..1..Cell.3.RPKM. 8cell 0.753074916100457 8cell -48 Morulae..1..Cell.4.RPKM. 16cell 0.975984157933152 16cell -49 Morulae..1..Cell.5.RPKM. 16cell 0.978965252255204 16cell -50 Morulae..1..Cell.6.RPKM. 16cell 0.972542473750977 16cell -51 Morulae..1..Cell.7.RPKM. 16cell 0.980084685003656 16cell -52 Morulae..1..Cell.8.RPKM. 8cell 0.701585854974489 8cell -53 Morulae..2..Cell.1.RPKM. 16cell 0.980419529105244 16cell -54 Morulae..2..Cell.2.RPKM. 16cell 0.980851332000861 16cell -55 Morulae..2..Cell.3.RPKM. 16cell 0.964267219512788 16cell -56 Morulae..2..Cell.4.RPKM. 16cell 0.957787782168123 16cell -57 Morulae..2..Cell.5.RPKM. 16cell 0.965485721368535 16cell -58 Morulae..2..Cell.6.RPKM. 16cell 0.957697139912933 16cell -59 Morulae..2..Cell.7.RPKM. 16cell 0.958777912908415 16cell -60 Morulae..2..Cell.8.RPKM. 16cell 0.973138715636811 16cell -61 Late.blastocyst..1..Cell.1.RPKM. blast 0.946030792526566 blast -62 Late.blastocyst..1..Cell.2.RPKM. blast 0.962138004343889 blast -63 Late.blastocyst..1..Cell.3.RPKM. blast 0.950748704451565 blast -64 Late.blastocyst..1..Cell.4.RPKM. blast 0.957227580718105 blast -65 Late.blastocyst..1..Cell.5.RPKM. blast 0.95434894493587 blast -66 Late.blastocyst..1..Cell.6.RPKM. blast 0.955943421895937 blast -67 Late.blastocyst..1..Cell.7.RPKM. blast 0.956356985705706 blast -68 Late.blastocyst..1..Cell.8.RPKM. blast 0.970493175210153 blast -69 Late.blastocyst..1..Cell.9.RPKM. blast 0.945326349715578 blast -70 Late.blastocyst..1..Cell.10.RPKM. blast 0.956481724858848 blast -71 Late.blastocyst..1..Cell.11.RPKM. blast 0.956159281369748 blast -72 Late.blastocyst..1..Cell.12.RPKM. blast 0.96425809974187 blast -73 Late.blastocyst..2..Cell.1.RPKM. blast 0.954566650006314 blast -74 Late.blastocyst..2..Cell.2.RPKM. blast 0.859795704593317 blast -75 Late.blastocyst..2..Cell.3.RPKM. blast 0.881194674798541 blast -76 Late.blastocyst..2..Cell.4.RPKM. blast 0.96703530306384 blast -77 Late.blastocyst..2..Cell.5.RPKM. blast 0.958079246177835 blast -78 Late.blastocyst..2..Cell.6.RPKM. blast 0.959780240457135 blast -79 Late.blastocyst..2..Cell.7.RPKM. blast 0.957562095748124 blast -80 Late.blastocyst..2..Cell.8.RPKM. blast 0.908172032074667 blast -81 Late.blastocyst..2..Cell.9.RPKM. blast 0.958716824617989 blast -82 Late.blastocyst..2..Cell.10.RPKM. blast 0.966000611704395 blast -83 Late.blastocyst..3..Cell.1.RPKM. blast 0.830150497819373 blast -84 Late.blastocyst..3..Cell.2.RPKM. blast 0.894937328405391 blast -85 Late.blastocyst..3..Cell.3.RPKM. blast 0.948131108497039 blast -86 Late.blastocyst..3..Cell.4.RPKM. blast 0.832148158277939 blast -87 Late.blastocyst..3..Cell.5.RPKM. blast 0.840068518192648 blast -88 Late.blastocyst..3..Cell.6.RPKM. blast 0.923562228265187 blast -89 Late.blastocyst..3..Cell.7.RPKM. blast 0.9377231069535 blast -90 Late.blastocyst..3..Cell.8.RPKM. blast 0.917408664281774 blast |
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