Mercurial > repos > artbio > gsc_high_dimensions_visualisation

changeset 6:19bef589f876 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit ee5de0b259c9b50872bb6f5f946e439345838349"
author artbio
date Wed, 24 Jun 2020 06:22:53 -0400
parents 569334568afa
children 18a1dc4aec4a
files high_dim_visu.R high_dim_visu.xml test-data/tsne-2.coord.tab test-data/tsne-2.nolabels.pdf
diffstat 4 files changed, 1038 insertions(+), 1038 deletions(-) [+]
line wrap: on
line diff
--- a/high_dim_visu.R	Mon Sep 02 04:39:20 2019 -0400
+++ b/high_dim_visu.R	Wed Jun 24 06:22:53 2020 -0400
@@ -278,7 +278,7 @@
 }
 
 
-data = read.table(
+data = read.delim(
   opt$data,
   check.names = FALSE,
   header = opt$colnames,
--- a/high_dim_visu.xml	Mon Sep 02 04:39:20 2019 -0400
+++ b/high_dim_visu.xml	Wed Jun 24 06:22:53 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="high_dimensions_visualisation" name="Generate PCA, tSNE and HCPC" version="0.9.5">
+<tool id="high_dimensions_visualisation" name="Generate PCA, tSNE and HCPC" version="0.9.6">
     <description>from highly dimensional expression data</description>
     <requirements>
         <requirement type="package" version="1.6.2=r35h6115d3f_0">r-optparse</requirement>
@@ -7,7 +7,7 @@
         <requirement type="package" version="0.15=r351he1b5a44_0">r-rtsne</requirement>
         <requirement type="package" version="0.4.7=r351h6115d3f_0">r-ggfortify</requirement>
         <requirement type="package" version="1.1.9=r351h0357c0b_0">r-clusterr</requirement>
-        <!--<requirement type="package" version="1.11.6=r351hc070d10_0">r-data.table</requirement>-->
+        <!-- <requirement type="package" version="1.11.6=r351hc070d10_0">r-data.table</requirement> -->
     </requirements>
     <stdio>
         <exit_code range="1:" level="fatal" description="Tool exception" />
@@ -378,8 +378,8 @@
             <param name="Rtsne_perplexity" value="10"/>
             <param name="Rtsne_theta" value="1" />
             <param name="Rtsne_normalize" value="FALSE" />
-            <output name="pdf_out" file="tsne-2.nolabels.pdf" ftype="pdf" compare="sim_size" delta="500"/>
-            <output name="table_coordinates" file="tsne-2.coord.tab" ftype="tabular" compare="sim_size" delta="500"/>
+            <output name="pdf_out" file="tsne-2.nolabels.pdf" ftype="pdf" compare="sim_size" delta="1000"/>
+            <output name="table_coordinates" file="tsne-2.coord.tab" ftype="tabular" compare="sim_size" delta="1000"/>
         </test>
     </tests>
     <help>
--- a/test-data/tsne-2.coord.tab	Mon Sep 02 04:39:20 2019 -0400
+++ b/test-data/tsne-2.coord.tab	Wed Jun 24 06:22:53 2020 -0400
@@ -1,1034 +1,1034 @@
 Cells	DIM1	DIM2	DIM3
-1001000173.G8	-11.370887	-11.298476	2.621264
-1001000173.B4	-17.126662	6.952232	-9.879715
-1001000173.A2	1.199914	-2.89011	-17.428673
-1001000173.E2	-0.121312	-10.634663	-4.97458
-1001000173.F6	7.670528	-14.769499	-10.491671
-1001000173.B12	-20.765321	-0.253502	-11.769811
-1001000173.H1	-6.90609	1.070903	-25.371105
-1001000173.E4	-15.2299	-11.642443	4.829602
-1001000173.C2	-0.662124	-2.932158	-24.861092
-1001000173.F4	-0.745721	-2.756011	-25.082597
-1001000173.E10	-0.767365	-2.820974	-25.047442
-1001000173.E6	-6.101916	-5.650931	-21.594808
-1001000173.C4	-5.685195	-8.995897	0.607138
-1001000173.B10	-0.76065	-2.811214	-25.161652
-1001000173.A7	-4.273207	-11.38671	22.355472
-1001000173.B8	1.008745	-7.523095	-21.687472
-1001000173.F9	9.48198	13.311241	2.580219
-1001000173.G6	-11.337759	-12.904664	6.817117
-1001000173.A9	-16.170556	-10.578076	-4.154364
-1001000173.D2	-16.487732	15.893345	-12.795243
-1001000173.F2	-2.114554	-16.342172	-3.141445
-1001000173.H9	-20.406785	-4.201691	-7.944175
-1001000173.G1	-10.528076	-14.99904	-5.24346
-1001000173.B3	-13.987697	12.292889	-10.786721
-1001000173.D7	-14.616053	1.857277	-10.511803
-1001000173.A12	0.27056	-7.895812	-21.9549
-1001000173.C1	-16.985241	-0.796852	-6.89928
-1001000173.H7	-0.771996	-2.828559	-25.038518
-1001000173.H5	1.055568	-2.60067	-20.761278
-1001000173.G2	-16.686884	16.291478	-5.065536
-1001000173.A3	-13.881563	-0.047488	-12.753972
-1001000173.D3	-0.729682	-2.771258	-25.099659
-1001000173.E1	-19.34446	11.768429	-12.235793
-1001000173.G12	-19.531343	11.610656	-12.137243
-1001000173.C10	-0.655772	-2.766846	-25.238074
-1001000173.C3	-8.791393	-12.594586	-4.293936
-1001000173.A5	-0.705297	-2.927211	-24.826505
-1001000173.G4	-16.445412	4.472225	-6.556946
-1001000173.B11	-11.728803	-0.005311	-12.138251
-1001000173.G9	-2.062222	-6.501813	-19.551959
-1001000173.F1	-3.201585	-6.619799	-19.390158
-1001000173.D8	-6.911861	1.088813	-25.349219
-1001000173.E12	-0.745057	-2.734507	-25.091884
-1001000173.F11	-18.535131	9.554508	-15.722123
-1001000173.E5	-13.184336	13.073837	-9.056027
-1001000173.G10	17.331693	6.044925	2.920269
-1001000173.B9	-19.444792	11.683653	-11.94483
-1001000173.C7	-19.727051	-8.568513	-0.116832
-1001000173.B2	-0.618615	-2.915774	-24.80219
-1001000173.H4	-14.458424	-12.249293	5.046685
-1001000174.G5	-20.786309	-0.344462	-11.666442
-1001000174.H9	1.917298	-6.779003	-21.095375
-1001000174.A10	-0.750671	-2.713433	-25.229934
-1001000174.G10	-2.018462	-16.31214	-3.128493
-1001000174.C8	-17.415866	-1.639325	-16.042823
-1001000174.F6	-0.698537	-2.845752	-25.162871
-1001000174.B4	0.441288	-7.607505	6.270975
-1001000174.H7	-7.559725	15.836893	4.122812
-1001000174.E10	-13.132789	-11.652405	4.801045
-1001000174.D5	-2.588281	-9.18992	5.298426
-1001000174.E5	-5.14068	-15.497555	0.514986
-1001000174.B11	-18.623996	-7.000601	0.017912
-1001000174.F10	-0.665758	-2.884827	-24.962585
-1001000174.A5	-6.597995	0.897515	-25.432156
-1001000174.B8	0.894163	-2.585495	-20.853825
-1001000174.F2	-14.067114	-5.754898	-13.132123
-1001000174.F9	-19.445403	11.7359	-12.272749
-1001000174.F4	-0.555999	-9.239035	-6.675979
-1001000174.B6	-18.699052	-6.60711	-0.116756
-1001000174.E2	-19.926335	-3.57208	-7.802405
-1001000174.G2	1.753589	-10.212568	-7.197919
-1001000174.D8	-18.661132	-6.254463	-0.074591
-1001000174.H6	-13.668025	16.319315	-9.720982
-1001000174.C3	9.940939	14.199216	2.046363
-1001000174.B7	-4.285036	-11.483515	1.119458
-1001000174.A7	-0.797025	-7.957696	-22.142381
-1001000174.H10	-13.144247	17.428719	-9.871272
-1001000174.F7	-20.73509	-4.16516	-10.358416
-1001000174.A2	5.797695	-14.366762	-11.094285
-1001000174.E4	-10.888946	-15.422062	-5.977295
-1001000174.D12	10.569833	-7.333114	0.474384
-1001000174.H4	-0.732054	-2.801817	-25.140609
-1001000174.C5	-14.196128	19.06099	-0.270851
-1001000174.E9	4.810906	13.294606	-4.141963
-1001000174.D1	-17.607628	-1.438026	-9.308235
-1001000174.G4	-16.155831	-10.462006	-4.703364
-1001000174.G9	-16.422902	0.295818	-13.591674
-1001000174.D4	-13.714179	11.909454	-14.999471
-1001000174.H11	-16.190587	-0.381605	-9.569412
-1001000174.A9	-19.815204	-3.101313	-8.004626
-1001000174.A4	-16.565035	-10.207398	4.175531
-1001000174.C7	-17.0793	2.115607	-5.786562
-1001000174.D11	9.99608	14.380619	1.926475
-1001000174.F5	-12.489128	-11.05596	0.091763
-1001000174.G6	-12.352915	-11.914758	-0.184494
-1001000174.D6	1.547833	-8.292358	-2.908173
-1001000174.H3	-19.806891	-3.141219	-8.019115
-1001000174.F12	9.517753	-9.412433	-6.110893
-1001000174.E6	0.388376	-7.517402	6.466978
-1001000174.G3	-0.674629	-2.756136	-25.107573
-1001000174.A8	-10.412765	8.538314	4.277415
-1001000174.B10	-0.724939	-2.822215	-25.24174
-1001000174.C2	-15.682609	3.458129	-19.49884
-1001000174.F1	-17.762076	5.241154	-6.638001
-1001000174.C11	-13.569077	-2.140475	-13.401747
-1001000174.H8	0.286213	-9.616086	-5.381414
-1001000174.H1	-0.07126	-3.311936	-25.258286
-1001000174.G8	1.370461	-8.885942	4.922045
-1001000174.B5	-0.690977	-2.793297	-25.168129
-1001000174.E11	-7.005599	-5.330413	-21.60185
-1001000174.E8	-17.035455	-8.463571	-5.201838
-1001000174.F11	-5.703967	-15.242022	-1.319911
-1001000174.A1	26.054558	-8.779897	1.165213
-1001000174.E7	-16.929736	4.139238	-18.386713
-1001000174.B1	-12.649058	-11.132506	0.05321
-1001000174.C12	-0.016736	-10.259921	-5.75878
-1001000174.C9	-13.725984	0.016523	-12.77123
-1001000174.D7	0.174525	-3.311474	-22.456938
-1001000174.D2	-14.004445	12.25858	-15.356877
-1001000174.C4	-14.32184	-1.773625	-12.309838
-1001000174.F8	-17.878986	-4.338875	-10.087325
-1001000174.D10	-16.37521	7.520442	-9.743384
-1001000174.G11	-12.520102	11.61738	-15.469508
-1001000174.A3	-7.68491	-16.256357	-6.118638
-1001000174.E3	-13.926571	12.215983	-10.714805
-1001000174.H5	-7.679779	9.399809	-18.984724
-1001000174.C6	-1.167571	-3.046918	8.568357
-1001000174.D3	-6.425721	-7.695756	-0.192006
-1001000174.D9	-16.162256	-10.51825	-4.291776
-1001000175.E1	-6.390833	-5.313584	-21.589619
-1001000175.A3	-1.982192	-16.520755	-3.278034
-1001000175.C11	-18.701412	-6.880963	0.024145
-1001000175.F3	-8.34184	-15.750808	-6.30438
-1001000175.B9	-0.242362	-3.156069	-25.262736
-1001000175.H4	-12.293862	-11.402528	-0.00308
-1001000175.G2	-19.961508	-8.798244	-0.063008
-1001000175.G11	-1.988213	-16.493694	-3.278768
-1001000175.B4	-17.760542	-2.026497	-7.253943
-1001000175.D2	-20.65492	-2.641492	-10.135031
-1001000175.C1	-6.230687	-7.787598	0.060486
-1001000175.G7	-13.638746	1.376396	-10.745388
-1001000175.E8	-17.972493	-8.21304	-4.237623
-1001000175.F6	-0.16829	-3.283126	-25.135625
-1001000175.H6	-0.731009	-2.766306	-25.100398
-1001000175.C7	-14.20366	19.10685	-0.333315
-1001000175.A11	-16.083757	12.233339	-9.591267
-1001000175.G8	-1.989814	-16.429189	-3.234794
-1001000175.A7	7.537157	-15.213836	-6.280315
-1001000175.H5	-0.733399	-2.836739	-25.157816
-1001000175.F8	1.066749	-2.519653	-20.712249
-1001000175.D12	-18.732379	-2.215576	-9.215943
-1001000175.A5	-2.408822	-9.573699	4.823403
-1001000175.D4	-2.033786	-16.468909	-3.26588
-1001000175.D10	2.636256	-7.789617	-3.969305
-1001000175.A9	-2.016077	-16.366643	-3.12913
-1001000175.H7	-10.971961	-12.99056	-1.579321
-1001000175.B1	-0.668033	-2.934926	-24.85824
-1001000175.D5	0.690373	-7.529505	-22.023482
-1001000175.C5	-11.661571	-14.095425	4.61273
-1001000175.B12	-7.196006	-7.822834	-0.232681
-1001000175.E3	-0.743324	-2.785295	-25.075409
-1001000175.F11	1.009713	-2.558167	-20.850058
-1001000175.G4	-2.000107	-16.488965	-3.273469
-1001000175.C4	-6.850704	-15.937426	-2.84562
-1001000175.F9	-17.057747	11.070235	-11.769114
-1001000175.E7	-13.756074	14.314567	-16.929054
-1001000175.E4	-21.049218	0.72088	-12.788271
-1001000175.G1	8.679676	12.367308	3.691272
-1001000175.B10	-13.796574	5.544416	-9.327683
-1001000175.C10	16.637722	-9.839233	11.714475
-1001000175.B5	-13.825069	-0.081411	-12.899107
-1001000175.D1	-15.524188	-5.961793	-8.373052
-1001000175.C2	-7.962151	-13.981459	-0.298312
-1001000175.F4	-2.160721	-9.264519	-0.449816
-1001000175.E2	16.057101	5.41254	3.847125
-1001000175.H3	1.889671	-8.57125	-4.542453
-1001000175.A4	-10.798931	8.694602	-11.739769
-1001000175.C12	-12.430664	-11.573009	-0.074479
-1001000175.G10	-12.517056	-11.52301	-0.294797
-1001000175.F2	-17.122904	19.608323	-3.156697
-1001000175.D11	7.35017	15.934427	7.858041
-1001000175.F5	-4.673961	-9.279335	16.045279
-1001000175.C8	-0.81204	-2.733412	-25.203645
-1001000175.F12	7.17556	15.970049	6.589537
-1001000175.D3	-3.550016	-6.805872	-19.428198
-1001000175.C9	1.892415	-1.453923	-18.765641
-1001000175.D6	-20.80438	-0.411233	-11.653039
-1001000175.E6	-1.989374	-16.38943	-3.133217
-1001000175.A6	-14.046955	-10.622423	0.776695
-1001000175.H8	26.073021	-8.768488	1.167907
-1001000175.B2	-12.968408	7.25301	-8.018899
-1001000175.B11	-18.611226	-7.036442	0.009596
-1001000175.E10	6.947731	-14.089152	-10.507906
-1001000175.D8	-3.950871	-7.942163	2.232127
-1001000175.F10	-15.22907	14.017257	-15.94024
-1001000175.E9	-3.650472	-8.553053	-20.19381
-1001000175.F7	-5.121046	9.986693	1.315911
-1001000175.G3	-14.189869	19.123019	-0.353628
-1001000175.C6	-5.390493	-15.477226	0.656622
-1001000175.E12	9.99875	12.610295	3.133776
-1001000175.A12	6.864691	-13.234781	-11.436921
-1001000175.A8	-20.297296	-0.264704	-11.717281
-1001000179.B12	0.585869	-7.990618	5.909518
-1001000180.A11	7.16573	17.050721	4.396564
-1001000180.E10	4.004084	16.873116	-5.016493
-1001000180.A5	15.243384	6.065382	3.273754
-1001000180.D2	6.288712	18.32496	0.239296
-1001000180.D8	5.076386	15.787727	-3.52199
-1001000180.E1	4.35131	-6.075568	-4.127678
-1001000180.F4	5.416651	16.56297	7.59123
-1001000180.H3	-18.397382	14.829391	-1.145117
-1001000180.D11	7.03612	17.027217	4.249304
-1001000180.B3	5.883128	16.370365	-2.607768
-1001000180.A4	3.686103	-6.768307	-4.10467
-1001000180.F12	4.30394	16.410209	-4.525632
-1001000180.E6	7.726847	15.558658	4.443
-1001000180.G1	10.453443	12.169005	6.024395
-1001000180.A9	6.295987	18.290216	0.235446
-1001000181.A3	6.287202	18.323136	0.244089
-1001000181.E6	-0.665686	-2.823162	-25.285174
-1001000181.D5	6.249164	18.331449	0.130689
-1001000181.D10	6.282512	18.326697	0.203554
-1001000181.F10	11.917517	12.916613	6.536742
-1001000181.C11	-6.162519	-5.921292	-21.520859
-1001000181.C6	-0.646495	-2.636632	-25.040937
-1001000181.E12	6.284411	18.316257	0.247785
-1001000181.G6	6.28254	18.331605	0.241455
-1001000181.B4	0.30834	-3.524435	-25.427337
-1001000181.G8	7.012368	16.184995	5.893625
-1001000181.F2	6.276613	18.321864	0.229209
-1001000181.C7	-0.641559	-2.597579	-25.046777
-1001000182.A3	26.066711	-8.806641	1.163564
-1001000182.F4	-0.733604	-2.709741	-25.214753
-1001000182.G4	9.095623	-11.218303	-5.879909
-1001000182.E6	-0.742993	-2.69314	-25.156262
-1001000182.C3	-13.755456	5.071976	-7.79415
-1001000182.D1	0.957087	-2.617064	-20.699581
-1001000182.G10	-0.775991	-2.759138	-25.231932
-1001000182.C12	-11.005792	14.487926	-18.571502
-1001000182.D10	10.673798	11.414003	6.159304
-1001000182.A5	-18.764481	-6.472003	-0.199129
-1001000182.E8	-12.670072	-0.331574	-12.048901
-1001000182.B4	-19.769892	-8.595223	-0.162642
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