Galaxy |

Changeset 13:48400c291093 (2024-04-23)

Previous changeset 12:65b719530dd5 (2020-11-27) Next changeset 14:32ae4a600167 (2024-07-08)

Commit message:
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8350493268ce3ced12b1133b9b0f734a288deb75

modified:
scmap_macros.xml
scmap_scmap_cell.xml

added:
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

diff -r 65b719530dd5 -r 48400c291093 scmap_macros.xml
--- a/scmap_macros.xml Fri Nov 27 13:44:11 2020 +0000
+++ b/scmap_macros.xml Tue Apr 23 07:48:26 2024 +0000

[

@@ -1,10 +1,10 @@
<macros>
-    <token name="@TOOL_VERSION@">1.6.3</token>
+    <token name="@TOOL_VERSION@">1.6.4</token>
     <token name="@HELP@">More information can be found at https://bioconductor.org/packages/release/bioc/html/scmap.html</token>
     <token name="@PROFILE@">18.01</token>
     <xml name="requirements">
       <requirements>
-        <requirement type="package" version="0.0.11">scmap-cli</requirement>
+        <requirement type="package" version="0.1.0">scmap-cli</requirement>
             <yield/>
       </requirements>
     </xml>
@@ -15,6 +15,7 @@
     </xml>
     <token name="@VERSION_HISTORY@"><![CDATA[
**Version history**
+1.6.4+galaxy0: Update scmap-cli to 0.1.0
1.6.3+galaxy0: Update scmap-cli to 0.0.11
1.6.2+galaxy0: Update scmap-cli to 0.0.10
1.6.1+galaxy0: Update scmap-cli to 0.0.9.

diff -r 65b719530dd5 -r 48400c291093 scmap_scmap_cell.xml
--- a/scmap_scmap_cell.xml Fri Nov 27 13:44:11 2020 +0000
+++ b/scmap_scmap_cell.xml Tue Apr 23 07:48:26 2024 +0000

[

@@ -9,6 +9,8 @@
             -i '$index_single_cell_experiment'
             -p '$project_single_cell_experiment'
             --number-nearest-neighbours '$n_nearest_neighbours'
+            --nearest-neighbours-threshold '$nearest_neighbours_threshold'
+            --threshold '$threshold'
             --cluster-col '${cluster_projection.cluster_col}'
             --output-object-file '$output_single_cell_experiment'
             --closest-cells-text-file '$closest_cells_text_file'
@@ -21,6 +23,8 @@
       <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." />
       <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'" />
       <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" />
+      <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." />
+      <param name="threshold" type="integer" label="Similarity threshold" value='0.7' help="Threshold on similarity (or probability for SVM and RF)." />
      <conditional name="cluster_projection">
         <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."/>
         <when value="true" >
@@ -43,12 +47,29 @@
         <test>
             <param name="index_single_cell_experiment" value="index_cell.rds" ftype="rdata"/>
             <param name="project_single_cell_experiment" value="test_sce_processed.rds" ftype="rdata"/>
-            <param name="cluster_projection" value="true" />
+            <conditional name="cluster_projection">
+                <param name="do_cluster_projection" value="true" />
+                <param name="cluster_col" value="cell_type1" />
+            </conditional>
             <output name="output_single_cell_experiment" file="closest_cells_clusters.rds" compare="sim_size"/>
             <output name="closest_cells_clusters_csv" file="closest_cells_clusters.tsv" compare="sim_size" />
             <output name="closest_cells_text_file" file="closest_cells.tsv" compare="sim_size"/>
             <output name="closest_cells_similarities_text_file" file="closest_cells_similarities.tsv" compare="sim_size"/>
         </test>
+        <test>
+            <param name="index_single_cell_experiment" value="index_cell.rds" ftype="rdata"/>
+            <param name="project_single_cell_experiment" value="test_sce_processed.rds" ftype="rdata"/>
+            <conditional name="cluster_projection">
+                <param name="do_cluster_projection" value="true" />
+                <param name="cluster_col" value="cell_type1" />
+            </conditional>
+            <param name="nearest_neighbours_threshold" value="3" />
+            <param name="threshold" value="0.5" />
+            <output name="output_single_cell_experiment" file="closest_cells_clusters_copy.rds" compare="sim_size"/>
+            <output name="closest_cells_clusters_csv" file="closest_cells_clusters_copy.tsv" compare="sim_size" />
+            <output name="closest_cells_text_file" file="closest_cells_copy.tsv" compare="sim_size"/>
+            <output name="closest_cells_similarities_text_file" file="closest_cells_similarities_copy.tsv" compare="sim_size"/>
+        </test>
     </tests>
     <help><![CDATA[
     @HELP@

diff -r 65b719530dd5 -r 48400c291093 test-data/closest_cells.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/closest_cells.csv Tue Apr 23 07:48:26 2024 +0000

@@ -0,0 +1,6 @@
+,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

diff -r 65b719530dd5 -r 48400c291093 test-data/closest_cells_clusters.rds

Binary file test-data/closest_cells_clusters.rds has changed

diff -r 65b719530dd5 -r 48400c291093 test-data/closest_cells_clusters.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/closest_cells_clusters.tsv Tue Apr 23 07:48:26 2024 +0000

@@ -0,0 +1,91 @@
+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

diff -r 65b719530dd5 -r 48400c291093 test-data/closest_cells_similarities.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/closest_cells_similarities.csv Tue Apr 23 07:48:26 2024 +0000

b'@@ -0,0 +1,6 @@\n+,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.\n+1,0.974273699811975,0.973659311436167,0.974854220234444,0.97839753346497,0.979490174962032,0.980115537598401,0.976313835558767,0.976881116973313,0.975901392182175,0.977322845448825,0.976323350516014,0.976971559860292,0.976320366157395,0.969912061538871,0.968501468487668,0.971522498841011,0.964951572472287,0.972748756493633,0.971942905027406,0.972017001342311,0.980520343865064,0.978080837270881,0.980078705456514,0.979798181564745,0.966241474136935,0.969158473501728,0.968707192268454,0.969841095031548,0.974854612410912,0.976503242175562,0.979804630823918,0.976544473170974,0.969481019998013,0.976489477308787,0.979995497607925,0.979854110006233,0.981867832635268,0.974786591856287,0.973765988696476,0.977837020195143,0.982102656773436,0.970638900011281,0.974968488962187,0.969481110283021,0.950812756659853,0.96807907709823,0.91630840568286,0.970572967922616,0.969146983045072,0.963005588968003,0.972427039750112,0.726218083982927,0.969017360461502,0.974170553961338,0.964279804847546,0.957081439198935,0.956990695530537,0.947526173473035,0.961646669180513,0.963312355197477,0.929414192606584,0.945349776265469,0.931894436659203,0.928302728076479,0.93495880629305,0.928964466633903,0.935785405180646,0.946332771937332,0.944210967521674,0.935446129048361,0.957020095156881,0.936513899155052,0.941244285216586,'..b'549,0.970520527970828,0.968478100687963,0.964493691190741,0.972285524744667,0.724424734546886,0.969559396842649,0.969364813048294,0.958239742574716,0.944755601653579,0.959029210899153,0.968964013352534,0.963723725469498,0.960711969960917,0.949879991563679,0.942457767725231,0.950427652531018,0.948091129226388,0.935725154213454,0.947068372664074,0.932792955705649,0.939589564737004,0.929847717771756,0.950599081967672,0.940231698364827,0.939390494922626,0.938175389389597,0.892258057827176,0.926372907311768,0.95245650968153,0.922841768364733,0.937416110024372,0.933878349854862,0.878774403798334,0.944167607789112,0.9386829330418,0.830037046627661,0.883713143953103,0.928636951069851,0.91354245801598,0.86465693599049,0.905142929288076,0.911070328984465,0.90368380440602\n+4,0.969539415685062,0.968605789622234,0.969975869820421,0.978880784666248,0.979406018332084,0.979819636687998,0.976293636860104,0.976907817743082,0.975961272994989,0.977298240230832,0.976152456170403,0.977158123689469,0.9755049070930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diff -r 65b719530dd5 -r 48400c291093 test-data/index_cell.rds

Binary file test-data/index_cell.rds has changed

diff -r 65b719530dd5 -r 48400c291093 test-data/index_cluster.png

Binary file test-data/index_cluster.png has changed

diff -r 65b719530dd5 -r 48400c291093 test-data/index_cluster.rds

Binary file test-data/index_cluster.rds has changed

diff -r 65b719530dd5 -r 48400c291093 test-data/project_cluster.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/project_cluster.csv Tue Apr 23 07:48:26 2024 +0000

@@ -0,0 +1,91 @@
+,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
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+11,X2.cell.embryo.3..Cell.1.RPKM.,2cell,0.997663075228921,2cell
+12,X2.cell.embryo.3..Cell.2.RPKM.,2cell,0.99770244480819,2cell
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diff -r 65b719530dd5 -r 48400c291093 test-data/project_cluster.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/project_cluster.tsv Tue Apr 23 07:48:26 2024 +0000

@@ -0,0 +1,91 @@
+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
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+12 X2.cell.embryo.3..Cell.2.RPKM. 2cell 0.99770244480819 2cell
+13 X4.cell.embryo.1..Cell.1.RPKM. 4cell 0.990134433448036 4cell
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+16 X4.cell.embryo.1..Cell.4.RPKM. 4cell 0.986969369421969 4cell
+17 X4.cell.embryo.2..Cell.1.RPKM. 4cell 0.978600490705419 4cell
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+24 X4.cell.embryo.3..Cell.4.RPKM. 4cell 0.995423880082539 4cell
+25 X8.cell.embryo.1..Cell.1.RPKM. unassigned 0.589322049052091 unassigned
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+31 X8.cell.embryo.2..Cell.3.RPKM. 8cell 0.986839564389094 8cell
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+35 X8.cell.embryo.2..Cell.7.RPKM. 8cell 0.976238026438341 8cell
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+42 X8.cell.embryo.3..Cell.6.RPKM. 8cell 0.96962809093506 8cell
+43 X8.cell.embryo.3..Cell.7.RPKM. 8cell 0.980186666445985 8cell
+44 X8.cell.embryo.3..Cell.8.RPKM. 8cell 0.965226853665217 8cell
+45 Morulae..1..Cell.1.RPKM. 16cell 0.950320842050556 16cell
+46 Morulae..1..Cell.2.RPKM. 16cell 0.979324688404905 16cell
+47 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
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+57 Morulae..2..Cell.5.RPKM. 16cell 0.965485721368535 16cell
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+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
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+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
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+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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