Mercurial > repos > ebi-gxa > scmap_scmap_cell

changeset 13:48400c291093 draft

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8350493268ce3ced12b1133b9b0f734a288deb75
author ebi-gxa
date Tue, 23 Apr 2024 07:48:26 +0000
parents 65b719530dd5
children 32ae4a600167
files scmap_macros.xml scmap_scmap_cell.xml 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
diffstat 15 files changed, 310 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- 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.
--- 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@
--- /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.
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+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
Binary file test-data/closest_cells_clusters.rds has changed
--- /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
--- /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
@@ -0,0 +1,6 @@
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Binary file test-data/index_cell.rds has changed
Binary file test-data/index_cluster.png has changed
Binary file test-data/index_cluster.rds has changed
--- /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
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+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
--- /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
+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	0.986969369421969	4cell
+17	X4.cell.embryo.2..Cell.1.RPKM.	4cell	0.978600490705419	4cell
+18	X4.cell.embryo.2..Cell.2.RPKM.	4cell	0.990517207278532	4cell
+19	X4.cell.embryo.2..Cell.3.RPKM.	4cell	0.986056209223088	4cell
+20	X4.cell.embryo.2..Cell.4.RPKM.	4cell	0.988962130990086	4cell
+21	X4.cell.embryo.3..Cell.1.RPKM.	4cell	0.995116150658076	4cell
+22	X4.cell.embryo.3..Cell.2.RPKM.	4cell	0.99274523738472	4cell
+23	X4.cell.embryo.3..Cell.3.RPKM.	4cell	0.995763679518167	4cell
+24	X4.cell.embryo.3..Cell.4.RPKM.	4cell	0.995423880082539	4cell
+25	X8.cell.embryo.1..Cell.1.RPKM.	unassigned	0.589322049052091	unassigned
+26	X8.cell.embryo.1..Cell.2.RPKM.	8cell	0.927499839382219	8cell
+27	X8.cell.embryo.1..Cell.3.RPKM.	8cell	0.921141336301299	8cell
+28	X8.cell.embryo.1..Cell.4.RPKM.	unassigned	0.59175824082949	unassigned
+29	X8.cell.embryo.2..Cell.1.RPKM.	8cell	0.974849607680171	8cell
+30	X8.cell.embryo.2..Cell.2.RPKM.	8cell	0.985093729996275	8cell
+31	X8.cell.embryo.2..Cell.3.RPKM.	8cell	0.986839564389094	8cell
+32	X8.cell.embryo.2..Cell.4.RPKM.	8cell	0.96892413940019	8cell
+33	X8.cell.embryo.2..Cell.5.RPKM.	8cell	0.96431663761681	8cell
+34	X8.cell.embryo.2..Cell.6.RPKM.	8cell	0.97148526041646	8cell
+35	X8.cell.embryo.2..Cell.7.RPKM.	8cell	0.976238026438341	8cell
+36	X8.cell.embryo.2..Cell.8.RPKM.	8cell	0.980695252466275	8cell
+37	X8.cell.embryo.3..Cell.1.RPKM.	8cell	0.97966322970515	8cell
+38	X8.cell.embryo.3..Cell.2.RPKM.	8cell	0.975362675268717	8cell
+39	X8.cell.embryo.3..Cell.3.RPKM.	8cell	0.975167821442514	8cell
+40	X8.cell.embryo.3..Cell.4.RPKM.	8cell	0.982088540632061	8cell
+41	X8.cell.embryo.3..Cell.5.RPKM.	8cell	0.983236065207029	8cell
+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
+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
Binary file test-data/select_features.png has changed
Binary file test-data/select_features.rds has changed
Binary file test-data/test_sce.rds has changed
Binary file test-data/test_sce_processed.rds has changed