Mercurial > repos > ebi-gxa > scmap_scmap_cell

changeset 14:32ae4a600167 draft default tip

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9dbf2be568a0cea589fee8a42f070718d7966780-dirty
author ebi-gxa
date Mon, 08 Jul 2024 08:53:18 +0000
parents 48400c291093
children
files 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 14 files changed, 63 insertions(+), 308 deletions(-) [+]
line wrap: on
line diff
--- 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
@@ -1,30 +1,30 @@
-<tool id="scmap_scmap_cell" name="Scmap cell projection" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
+<tool id="scmap_scmap_cell" name="Scmap cell projection" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
     <description>searches each cell in a query dataset for the nearest neighbours by cosine distance within a collection of reference datasets.</description>
     <macros>
         <import>scmap_macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        scmap-scmap-cell.R 
-            -i '$index_single_cell_experiment' 
-            -p '$project_single_cell_experiment' 
-            --number-nearest-neighbours '$n_nearest_neighbours' 
+        scmap-scmap-cell.R
+            -i '$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 '$closest_cells_text_file' 
-            --closest-cells-similarities-text-file '$closest_cells_similarities_text_file'  
+            --cluster-col '${cluster_projection.cluster_col}'
+            --output-object-file '$output_single_cell_experiment'
+            --closest-cells-text-file '$closest_cells_text_file'
+            --closest-cells-similarities-text-file '$closest_cells_similarities_text_file'
             #if $cluster_projection
-            --output-clusters-text-file '$closest_cells_clusters_csv' 
-            #end if      
+            --output-clusters-text-file '$clusters_text_file'
+            #end if
       ]]></command>
     <inputs>
       <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)." />
+      <param name="threshold" type="float" 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" >
@@ -39,7 +39,7 @@
       <data name="output_single_cell_experiment" format="rdata" />
       <data name="closest_cells_text_file" format="tabular" />
       <data name="closest_cells_similarities_text_file" format="tabular" />
-      <data name="closest_cells_clusters_csv" format="tabular">
+      <data name="clusters_text_file" format="tabular">
         <filter>cluster_projection['do_cluster_projection']</filter>
       </data>
     </outputs>
@@ -52,9 +52,29 @@
                 <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"/>
+            <output name="clusters_text_file">
+                <assert_contents>
+                    <has_n_lines n="91" delta="1"/>
+                    <has_text_matching expression="Oocyte..1.RPKM.\tzygote\t0\.974.*\tzygote"/>
+                    <has_text_matching expression="Zygote..3.RPKM.\tunassigned\tNA\tunassigned"/>
+                    <has_text_matching expression="X2.cell.embryo.1..Cell.1.RPKM.\t2cell\t0\.976.*\t2cell"/>
+                    <has_text_matching expression="X4.cell.embryo.3..Cell.4.RPKM.\t4cell\t0\.979.*\t4cell"/>
+                    <has_text_matching expression="X8.cell.embryo.3..Cell.8.RPKM.\t8cell\t0\.973.*\t8cell"/>
+                    <has_text_matching expression="Morulae..2..Cell.8.RPKM.\t16cell\t0\.967.*\t16cell"/>
+                    <has_text_matching expression="Late.blastocyst..3..Cell.8.RPKM.\tblast\t0\.938.*\tblast"/>
+                </assert_contents>
+            </output>
+            <output name="closest_cells_text_file" file="closest_cells.tsv"/>
+            <output name="closest_cells_similarities_text_file">
+                <assert_contents>
+                    <has_n_lines n="6"/>
+                    <has_text_matching expression="1\t0\.974.*\t0\.974.*\t0\.726.*\t0\.922.*\t0\.909.*"/>
+                    <has_text_matching expression="2\t0\.974.*\t0\.973.*\t0\.726.*\t0\.922.*\t0\.938.*"/>
+                    <has_text_matching expression="3\t0\.974.*\t0\.973.*\t0\.724.*\t0\.911.*\t0\.903.*"/>
+                    <has_text_matching expression="4\t0\.969.*\t0\.968.*\t0\.768.*\t0\.947.*\t0\.919.*"/>
+                    <has_text_matching expression="5\t0\.969.*\t0\.968.*\t0\.769.*\t0\.925.*\t0\.917.*"/>
+                </assert_contents>
+            </output>
         </test>
         <test>
             <param name="index_single_cell_experiment" value="index_cell.rds" ftype="rdata"/>
@@ -63,17 +83,37 @@
                 <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"/>
+            <param name="nearest_neighbours_threshold" value="1" />
+            <param name="threshold" value="0.2" />
+            <output name="output_single_cell_experiment" file="closest_cells_clusters.rds" compare="sim_size"/>
+            <output name="clusters_text_file">
+                <assert_contents>
+                    <has_n_lines n="91" delta="1"/>
+                    <has_text_matching expression="Oocyte..1.RPKM.\tzygote\t0\.974.*\tzygote"/>
+                    <has_text_matching expression="Zygote..3.RPKM.\tzygote\t0\.980.*\tzygote"/>
+                    <has_text_matching expression="X2.cell.embryo.1..Cell.1.RPKM.\t2cell\t0\.976.*\t2cell"/>
+                    <has_text_matching expression="X4.cell.embryo.3..Cell.4.RPKM.\t4cell\t0\.979.*\t4cell"/>
+                    <has_text_matching expression="X8.cell.embryo.3..Cell.8.RPKM.\t8cell\t0\.973.*\t8cell"/>
+                    <has_text_matching expression="Morulae..2..Cell.8.RPKM.\t16cell\t0\.967.*\t16cell"/>
+                    <has_text_matching expression="Late.blastocyst..3..Cell.8.RPKM.\tblast\t0\.938.*\tblast"/>
+                </assert_contents>
+            </output>
+            <output name="closest_cells_text_file" file="closest_cells.tsv"/>
+            <output name="closest_cells_similarities_text_file">
+                <assert_contents>
+                    <has_n_lines n="6"/>
+                    <has_text_matching expression="1\t0\.974.*\t0\.974.*\t0\.726.*\t0\.922.*\t0\.909.*"/>
+                    <has_text_matching expression="2\t0\.974.*\t0\.973.*\t0\.726.*\t0\.922.*\t0\.938.*"/>
+                    <has_text_matching expression="3\t0\.974.*\t0\.973.*\t0\.724.*\t0\.911.*\t0\.903.*"/>
+                    <has_text_matching expression="4\t0\.969.*\t0\.968.*\t0\.768.*\t0\.947.*\t0\.919.*"/>
+                    <has_text_matching expression="5\t0\.969.*\t0\.968.*\t0\.769.*\t0\.925.*\t0\.917.*"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[
     @HELP@
-    
+
     @VERSION_HISTORY@
     ]]></help>
     <expand macro="citations" />
--- a/test-data/closest_cells.csv	Tue Apr 23 07:48:26 2024 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -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
Binary file test-data/closest_cells_clusters.rds has changed
--- 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
@@ -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
--- 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
@@ -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.
-1,0.974273699811975,0.973659311436167,0.974854220234444,0.97839753346497,0.979490174962032,0.980115537598401,0.976313835558767,0.976881116973313,0.975901392182175,0.977322845448825,0.976323350516014,0.976971559860292,0.976320366157395,0.969912061538871,0.968501468487668,0.971522498841011,0.964951572472287,0.972748756493633,0.971942905027406,0.972017001342311,0.980520343865064,0.978080837270881,0.980078705456514,0.979798181564745,0.966241474136935,0.969158473501728,0.968707192268454,0.969841095031548,0.974854612410912,0.976503242175562,0.979804630823918,0.976544473170974,0.969481019998013,0.976489477308787,0.979995497607925,0.979854110006233,0.981867832635268,0.974786591856287,0.973765988696476,0.977837020195143,0.982102656773436,0.970638900011281,0.974968488962187,0.969481110283021,0.950812756659853,0.96807907709823,0.91630840568286,0.970572967922616,0.969146983045072,0.963005588968003,0.972427039750112,0.726218083982927,0.969017360461502,0.974170553961338,0.964279804847546,0.957081439198935,0.956990695530537,0.947526173473035,0.961646669180513,0.963312355197477,0.929414192606584,0.945349776265469,0.931894436659203,0.928302728076479,0.93495880629305,0.928964466633903,0.935785405180646,0.946332771937332,0.944210967521674,0.935446129048361,0.957020095156881,0.936513899155052,0.941244285216586,0.869102684962689,0.880259691379051,0.937806497095698,0.924444477590199,0.937586715214649,0.931825507780561,0.881831453276571,0.926854415776569,0.941461737032717,0.819203455562143,0.918058912946314,0.932190630105853,0.860442649254729,0.858769171932451,0.899776457031776,0.922840962875508,0.909235395907432
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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
--- a/test-data/project_cluster.csv	Tue Apr 23 07:48:26 2024 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,91 +0,0 @@
-,cell,scmap_cluster_labs,scmap_cluster_siml,combined_labs
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-4,Zygote..1.RPKM.,2cell,0.993401179090721,2cell
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-11,X2.cell.embryo.3..Cell.1.RPKM.,2cell,0.997663075228921,2cell
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-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
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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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-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
--- a/test-data/project_cluster.tsv	Tue Apr 23 07:48:26 2024 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -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	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