# HG changeset patch
# User iuc
# Date 1671295988 0
# Node ID f005c350af7f355666bdbf46db9515faa61d09bf

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset commit 517bf38557204e91a3652046a9412fb635257c8f

diff -r 000000000000 -r f005c350af7f ggupset.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ggupset.xml	Sat Dec 17 16:53:08 2022 +0000
@@ -0,0 +1,54 @@
+<tool name="ggupset" id="emc-ggupset" version="1.0" profile="21.09">
+	<description>produces plots of relationships, similar to venn diagrams.</description>
+	<requirements>
+		<requirement type="package" version="0.3.0">r-ggupset</requirement>
+		<requirement type="package" version="1.3.2">r-tidyverse</requirement>
+	</requirements>
+	<command><![CDATA[
+#for $f in $input
+	ln -s '$f' '$f.element_identifier';
+#end for
+
+Rscript '$__tool_directory__/upset.R' '$n_int' '$x_lab' '$y_lab' '$width' '$height'
+#for $f in $input
+	'$f.element_identifier'
+#end for
+;
+]]></command>
+	<inputs>
+		<param name="input" type="data" format="txt,tabular" multiple="true" label="Gene List files" />
+		<param name="n_int" type="integer"  min="1" max="100" value="40" label="Numer of interactions to show"/>
+		<param name="x_lab" type="text"  value="Shared output across results" label="x-axis label"/>
+		<param name="y_lab" type="text"  value="Number of shared results" label="y-axis label"/>
+
+		<param name="width" type="integer" min="400" value="1000" label="Plot Width (px)"/>
+		<param name="height" type="integer" min="400" value="800" label="Plot Height (px)"/>
+	</inputs>
+	<outputs>
+		<data name="upset_freq" format="png" from_work_dir="upset-freq.png" label="${tool.name} on ${on_string}: Upset by frequency" />
+		<data name="upset_degree" format="png" from_work_dir="upset-degree.png" label="${tool.name} on ${on_string}: Upset by degree" />
+		<data name="commonalities" format="tabular" from_work_dir="upset.tsv" label="${tool.name} on ${on_string}: Identified Overlapping Groups" />
+	</outputs>
+	<tests>
+		<test>
+			<param name="input" value="HEP3B,HUH,JHH6,JHH7,SNU"/>
+			<param name="n_int" value="40"/>
+			<param name="width" value="1000"/>
+			<param name="height" value="800"/>
+			<output name="upset_degree" ftype="png" compare="sim_size">
+				<assert_contents>
+					<has_size value="82441" delta="10000" />
+				</assert_contents>
+			</output>
+			<output name="upset_freq" ftype="png" compare="sim_size">
+				<assert_contents>
+					<has_size value="81466" delta="10000" />
+				</assert_contents>
+			</output>
+			<output name="commonalities" file="upset.tsv" ftype="tabular"/>
+		</test>
+	</tests>
+	<help><![CDATA[
+`Upset plots <https://en.wikipedia.org/wiki/UpSet_Plot>`__ are a data visualisation similar to Venn diagrams, but extensible for many more than 3 sets.
+		]]></help>
+</tool>
diff -r 000000000000 -r f005c350af7f test-data/HEP3B
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/HEP3B	Sat Dec 17 16:53:08 2022 +0000
@@ -0,0 +1,957 @@
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diff -r 000000000000 -r f005c350af7f test-data/HUH
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/HUH	Sat Dec 17 16:53:08 2022 +0000
@@ -0,0 +1,155 @@
+SOST
+IGFBP2
+TRIM58
+AC079466.1
+LINC00488
+UGT2B15
+CHST11
+BMP6
+LINC01287
+EFNA5
+SH2D5
+LINC02535
+LINC02575
+AXIN2
+KIF7
+PTPRU
+SSBP2
+CTSS
+PRRT1B
+RP11-402P6.15
+PON1
+THBD
+HMGCS2
+ZNF114
+CACNA1D
+ITGB6
+NLRP2
+SLC17A4
+JUP
+RTL5
+TCF7
+SLC13A5
+TRIB3
+NR0B2
+RP11-318G21.4
+TMEM200B
+TMEM158
+SOX6
+KDM5B
+IL13RA2
+PIK3C2G
+SAMD12
+IRF8
+EDNRB
+AKR1C7P
+FAM155B
+XIST
+MAMLD1
+PBLD
+LINC02593
+SLC30A3
+LRRC61
+CLU
+TUB
+ERICH5
+PPFIA3
+RASAL1
+FOXF2
+ZBED6CL
+NLRC5
+GLT1D1
+LIPH
+HMOX1
+MIR9-1HG
+GDF7
+PTPRH
+SULF2
+ARL4C
+LINC02381
+CES1P1
+C3P1
+LRRC3
+TSPAN18
+REEP6
+BTC
+PAGE1
+FBXL17
+SOWAHB
+LINC01419
+RP11-284F21.10
+ARHGAP18
+CERCAM
+CYP3A5
+ELAPOR1
+BLNK
+CD82
+HOXA11
+ERBB2
+CLEC2L
+ANKRD20A7P
+NR4A1
+ODF2L
+C1orf116
+RP11-566K19.6
+TP53I11
+PKP3
+GLIS3
+SMAD9
+SEMA3G
+SLC29A4
+PRKCQ-AS1
+CCR1
+SNRPN
+ETFB
+RP11-402P6.9
+SPECC1-DT
+RP11-54O7.1
+DNMT3B
+DRAIC
+THSD7A
+CPNE7
+METTL24
+ZSCAN30
+COL7A1
+EGFR-AS1
+CDH23
+HPD
+CX3CL1
+LINC02889
+ATP8B2
+CPNE2
+ECM2
+ASIC1
+VWCE
+OLFM3
+C4BPA
+OSBPL10
+RP11-299H22.3
+NRP2
+ANXA13
+GATA3
+CARMAL
+KIF17
+MYO10
+TSPEAR-AS2
+BAZ2B
+MSI1
+MAB21L3
+ARRDC4
+HSD11B1L
+AC098826.5
+SHD
+LINC01515
+SUSD2
+DNAH5
+VSX1
+FAT3
+DEPP1
+RELN
+KIF12
+EML1
+TSPY2
+ZC3H6
+ZNF595
+SDSL
diff -r 000000000000 -r f005c350af7f test-data/JHH6
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/JHH6	Sat Dec 17 16:53:08 2022 +0000
@@ -0,0 +1,238 @@
+LINC00942
+CFH
+CD24
+MMP7
+SLC16A7
+PPL
+SLC7A2
+DTX1
+ADD3
+NNMT
+CARD11
+GSN
+SEMA3E
+S100A4
+DSP
+SKAP2
+PLPP2
+PCDH7
+SCN9A
+FN1
+PCSK1N
+CLDN2
+NDRG1
+TNS1
+AFF2
+ALDH3A1
+SPP1
+CD163L1
+TIMP3
+SGSH
+BASP1
+ZNF185
+ADORA1
+CLSTN2
+PPP1R9A
+LZTS1
+HOMER1
+GALNT6
+MSI2
+RP1-27K12.2
+ATP13A2
+HMGCS1
+NRK
+KCNK1
+RAVER2
+TUBA1A
+HIP1
+PTX3
+SHANK3
+ZNF727
+CHST9
+ARSI
+CHI3L1
+MSMO1
+LPP
+NR2F1
+UBASH3B
+CDC42BPG
+GDNF
+EBF4
+STOM
+ATP9B
+ITGB3
+BAMBI
+SORL1
+CORO2B
+SEMA6B
+TMEM71
+PPFIBP2
+ZBTB18
+ANXA10
+HMOX1
+IDI1
+FBXO32
+ELAVL2
+COL4A6
+NCAM1
+C1QL1
+ZNF716
+SV2A
+EDN2
+SHANK2
+NID1
+PEAR1
+VCAM1
+MYO15B
+NRIP1
+CNN1
+NEBL
+SEPTIN8
+CLDN11
+AMBP
+CLIC6
+MAN1A1
+CDKN1A
+ADAMTS10
+ELAPOR1
+TNXB
+MMP3
+PLEKHO1
+IL1RAPL1
+RAB38
+TPD52L1
+TCEA3
+PROM1
+SOD3
+LUM
+CACNA2D3
+DLG3
+PLAG1
+FAM89A
+HAS3
+ZNF697
+TMCC3
+RP5-1063M23.4
+GPNMB
+FAS
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+ITGBL1
+TMOD2
+RP11-47I22.3
+LINC00839
+SPECC1
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+CORO2A
+GUCY1A2
+BAGE2
+FNDC4
+SHISAL1
+PDP1
+CNTNAP3
+ANGPTL2
+GREM1
+SLC26A11
+ADTRP
+HR
+GJA3
+KCNMB4
+FAM160B1
+NBL1
+PCDH1
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+MAPK13
+HSD17B2
+GLP2R
+AK7
+CHMP4C
+ROBO1
+ATP8B1
+KCTD15
+CEBPA
+SLC25A18
+RUNX3
+TAGLN
+TMEM40
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+CNRIP1
+NMNAT2
+PODXL
+CDS1
+ST6GALNAC5
+HOMER2
+JAZF1
+F2R
+NCR3LG1
+GGT5
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+CRACDL
+LNCOG
+MX1
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+NCKAP5
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+ID1
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+REPS2
+CUBN
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+CACNB4
+FRMD4B
+SFN
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+MARCO
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+SYNC
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+ARL14
+ZSWIM5
+IL24
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+PAIP2B
+ALS2CL
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+SHROOM3
+MEIS3
+CRIP2
+CCRL2
+ADAMTS6
+BCYRN1
+AIF1L
diff -r 000000000000 -r f005c350af7f test-data/JHH7
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/JHH7	Sat Dec 17 16:53:08 2022 +0000
@@ -0,0 +1,299 @@
+NLRP1
+ANXA3
+TENM3
+KCNJ16
+TTR
+CEACAM6
+CDH1
+DPYSL3
+CDKN1A
+MITF
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+CTSZ
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+ZNF462
+CARD16
+GLYATL1
+KRT15
+TUSC3
+IL18
+GP2
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+AJUBA
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+CCNG2
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+ADGRD1
+ACSS2
+GBP1
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+PRRG4
+YPEL5
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+TAGLN
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+CASP1
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+ACHE
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+HLA-DRB1
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+SOD3
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+DHRS2
+CFAP69
+PRODH
+KCNMB3
+ZNF600
+NEURL1B
diff -r 000000000000 -r f005c350af7f test-data/SNU
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SNU	Sat Dec 17 16:53:08 2022 +0000
@@ -0,0 +1,858 @@
+MATN2
+CCL2
+LCP1
+ADAMTS14
+CDH6
+PADI2
+ZPLD1
+MYH16
+SCD
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+COBL
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+NUP210
+CCDC3
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+S100A6
+F3
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+TMPRSS15
+HPGD
+NCS1
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+LPCAT2
+PXDN
+MMP15
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+ABC10-44372100G24.1
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+PCSK1N
+GAS6-DT
+GABRG3
+FZD8
+LCAL1
+EPN2
+BEX4
+NAT8L
+CCRL2
+HID1
+GCNT3
+SCN1B
+TRPM4
+UPP1
+PDE4A
+NFASC
+CCDC88C
+PPARGC1B
+RGS20
+CD37
+SNTG2-AS1
+EREG
+CES1
+CCN3
+PGGHG
+TMEM171
+RPRM
+AC144450.1
+RP11-538D16.2
+TM4SF18
+ARHGAP24
+P2RY6
+DNASE1L1
+JCAD
+NR5A2
+SAMD3
+ZNF385D
+ANK2
+ADA
+CDIP1
+PID1
+MAP3K4-AS1
+AOAH
+THBS1-IT1
+TSPOAP1
+MYO3B
+TRPA1
+MGAM
+ANGPTL2
+LUCAT1
+EMP2
+RP11-572C21.1
+PCSK9
+ATOH8
+CTB-63M22.1
+ASIC1
+XKR6
+SPANXB1
+RP4-607I7.1
+CACHD1
+MIR503HG
+CRIP2
+RPS15P4
+HKDC1
+CALN1
+CACNG7
+RPL3P4
+FGFR4
+LAMA5
+LRP3
+SOWAHD
+WTAPP1
+PAPLN
+GRIA3
+DCHS1
+RP1
+PKIA
+HOXB5
+EMX2
+SYT14
+PRSS12
+SLC2A13
+GLDC
+TGIF2LY
+RP11-109P6.2
+MMP24
+TNFRSF11B
+KCNC4
+HCAR1
+LINC01106
+SLC7A14
+AREG
+SLC27A2
+LONRF2
+AF121898.3
+GS1-199J3.3
+SMARCD3
+SLITRK1
+SELENOP
+RP11-190A12.10
+MIR1915HG
+WLS
+DACT2
+RUNX3
+OPCML
+CALHM5
+MS4A4A
+SERPINA9
+LGR5
+RORA
+ADGRF4
+RAMP1
+GPC6
+SIRPG-AS1
+RP3-413H6.3
+VAC14-AS1
+CFH
+S100A4
+PPP1R14A
+IQCK
+MYH15
+RNF157
+MAPK11
+RP11-566H8.3
+PIGZ
+NANOS1
+RP5-1120P11.3
+ZNF295-AS1
+STK32B
+TUB
+RP11-244B22.11
+SLC4A8
+SCARF2
+GABRQ
+SLC29A2
+CCN4
+WASF3
+NAP1L3
+LZTS1
+MMP13
+SLC2A12
+JPH1
+FAM241A
+ZNF117
+LINC00327
+MERTK
+MTUS1
+CCDC80
+RP11-20J15.3
+CNR1
+SDC2
+THBS2
+KCNG1
+SMIM10
+ZFP92
+RP11-412N9.1
+RP13-143G15.4
+LAD1
+GNG2
+CA12
+RP11-2G1.1
+IGFBP4
+SYBU
+LINC00996
+SCAT8
+DSC2
+LINC02582
+TRPC4
+CIB2
+FAM110C
+CHI3L1
+ZFYVE28
+IGFBP3
+CXCL8
+CLDN3
+NQO1
+GYPC
+ABCC2
+FOXQ1
+PANX2
+SLC2A2
+SPNS2
+ZFPM2-AS1
+RP11-412P11.1
+LINC01721
+ABCA3
+MIR646HG
+ABCC9
+CTD-2091N23.1
+MAFB
+CTD-2003C8.2
+SERPINB7
+SHOC1
+RPL39P3
+BBC3
+SLC29A4
+CLDN11
+RP11-889D3.1
+FAM13A
+EPHX4
+IRX3
+ZNF804A
+FKBP1C
+AC144450.2
+RPL21P16
+IP6K3
+TUBAP13
+SBK2
+OSBP2
+IL1B
+LGI2
+STK31
+IL17RD
+SPTBN2
+SLC16A6
+AC006460.2
+RP11-301G19.1
+AC005083.1
+AP000221.1
+SLC38A4
+TNNT1
+HAPLN3
+MPP2
+TMEM59L
+KRT34
+RP4-665J23.4
+CTD-2297D10.2
+NTRK3
+ANK1
+CYP39A1
+USP2
+RP11-78C3.1
+SLC6A15
+GPC2
+LINC01098
+LAMA4
+SCAMP5
+MDK
+LINC00654
+RP11-11N9.4
+DAAM2
+RP11-438F14.11
+PTER
+LRRN4
+RUNX3-AS1
+SH3GL3
+EPCAM
+RP11-731J8.2
+AC073130.1
+FEZ1
+SHC3
+SYT11
+C4orf54
+LMOD1
+IL2RG
+CSPG4
+RP11-66B24.7
+RP11-1152H15.1
+FCHO1
+CLIP3
+TP73
+EFR3B
+TMEM25
+DMRT3
+PRAME
+GSTM4
+SLC16A9
+TGFA
+C2orf15
+HSD17B2
+BTG2
+RHPN1
+PCDHAC2
+THSD7A
+RP11-708B6.2
+LINC01602
+ZIC5
+COL21A1
+KC6
+PTGFRN
+SORCS1
+CTD-2334D19.1
+C9orf116
+ZBTB46
+TYMP
+ANGPTL4
diff -r 000000000000 -r f005c350af7f test-data/upset.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/upset.tsv	Sat Dec 17 16:53:08 2022 +0000
@@ -0,0 +1,2203 @@
+gene	files
+ABAT	HEP3B
+ABC10-44372100G24.1	SNU
+ABCA13	SNU
+ABCA3	SNU
+ABCB9	SNU
+ABCC2	SNU
+ABCC3	HEP3B
+ABCC9	SNU
+ABCG5	HEP3B
+ABCG8	HEP3B
+ABI3BP	HEP3B
+ABLIM2	HEP3B
+ABLIM3	HEP3B
+ABTB1	JHH7
+AC002456.2	HEP3B
+AC003092.1	SNU
+AC005083.1	SNU
+AC005301.9	SNU
+AC005307.1	SNU
+AC006460.2	HEP3B,SNU
+AC025171.1	HEP3B
+AC058791.1	HEP3B
+AC073130.1	SNU
+AC074289.1	HEP3B
+AC079466.1	HUH
+AC098826.5	HUH
+AC106869.2	HEP3B
+AC144450.1	SNU
+AC144450.2	SNU
+ACCS	HEP3B
+ACHE	JHH7
+ACKR3	JHH7,SNU
+ACOT12	HEP3B
+ACSL5	HEP3B
+ACSM2A	HEP3B
+ACSS1	SNU
+ACSS2	JHH7
+ACTBL2	SNU
+ACTR1B	SNU
+ADA	HEP3B,JHH6,SNU
+ADAM11	HEP3B
+ADAM15	SNU
+ADAM21	HEP3B
+ADAMTS10	HEP3B,JHH6,SNU
+ADAMTS12	HEP3B
+ADAMTS14	SNU
+ADAMTS16	SNU
+ADAMTS2	JHH6,SNU
+ADAMTS6	JHH6
+ADAMTS7	HEP3B,JHH6
+ADAMTS9	HEP3B,SNU
+ADAMTS9-AS1	HEP3B
+ADAMTSL2	HEP3B
+ADCY1	SNU
+ADCY3	HEP3B
+ADD3	JHH6
+ADGRD1	JHH7
+ADGRF4	SNU
+ADGRG5	HEP3B
+ADGRG6	HEP3B
+ADGRV1	HEP3B
+ADH4	HEP3B
+ADH6	HEP3B,JHH7
+ADM	SNU
+ADORA1	JHH6,SNU
+ADORA2B	SNU
+ADRB2	SNU
+ADTRP	JHH6,SNU
+AEBP1	HEP3B
+AF121898.3	SNU
+AFF2	JHH6
+AFF4	HEP3B
+AGA	SNU
+AGR2	HEP3B
+AGT	HEP3B
+AGTR1	HEP3B
+AGTR2	HEP3B
+AGXT	JHH7
+AHNAK	HEP3B,JHH7
+AHSG	HEP3B
+AIF1L	JHH6
+AIG1	HEP3B
+AJUBA	JHH7
+AK7	JHH6
+AKAP12	HEP3B,JHH7
+AKR1B1	HEP3B,SNU
+AKR1B10	HEP3B
+AKR1C1	SNU
+AKR1C7P	HUH
+AKR1D1	HEP3B,JHH7
+ALB	HEP3B,SNU
+ALDH1A2	HEP3B
+ALDH1L1	HEP3B
+ALDH3A1	JHH6
+ALDH3B1	HEP3B,JHH7
+ALDH5A1	SNU
+ALDH8A1	HEP3B
+ALKAL2	SNU
+ALOX12P2	HEP3B
+ALOX15P1	HEP3B
+ALPK2	SNU
+ALPP	JHH6,SNU
+ALS2CL	HEP3B,JHH6
+AMBP	JHH6
+AMOT	JHH7,SNU
+AMOTL2	JHH7
+ANGPTL1	HEP3B
+ANGPTL2	HEP3B,JHH6,SNU
+ANGPTL3	HEP3B,JHH7
+ANGPTL4	SNU
+ANGPTL8	JHH7
+ANK1	SNU
+ANK2	JHH6,SNU
+ANKRD13B	SNU
+ANKRD18B	HEP3B
+ANKRD20A7P	HUH
+ANKRD33B	HEP3B
+ANP32B	HEP3B
+ANXA10	HEP3B,JHH6,SNU
+ANXA13	HUH
+ANXA3	JHH7,SNU
+ANXA8	HEP3B,SNU
+ANXA8L1	HEP3B,SNU
+AOAH	SNU
+AP000221.1	SNU
+AP004372.1	SNU
+APBA2	SNU
+APBB1IP	HEP3B,SNU
+APBB2	HEP3B
+APC	HEP3B
+APELA	HEP3B
+APH1B	HEP3B
+APLP1	SNU
+APOBEC3B	SNU
+APOC2	HEP3B
+APOL2	HEP3B
+APOL6	HEP3B
+AQP1	HEP3B
+AQP4	JHH7
+ARAP3	SNU
+AREG	JHH7,SNU
+ARHGAP18	HUH
+ARHGAP24	SNU
+ARHGAP31	HEP3B
+ARHGAP40	HEP3B
+ARHGDIB	JHH7
+ARHGEF10L	SNU
+ARHGEF26-AS1	HEP3B
+ARHGEF28	HEP3B,SNU
+ARHGEF4	HEP3B
+ARHGEF6	SNU
+ARHGEF9	JHH6,SNU
+ARL14	JHH6
+ARL4C	HUH
+ARMC9	HEP3B
+ARMCX3	JHH7
+ARMH1	HEP3B
+ARMH4	HEP3B
+ARRB1	SNU
+ARRDC3	HEP3B
+ARRDC4	HUH
+ARSB	HEP3B
+ARSI	HEP3B,JHH6,SNU
+ARSJ	HEP3B
+ASB4	HEP3B
+ASB9	HEP3B
+ASIC1	HUH,SNU
+ASPA	JHH7
+ASPDH	HEP3B
+ASPHD1	HEP3B
+ASS1	SNU
+ATF5	JHH7
+ATOH8	HEP3B,SNU
+ATP10A	SNU
+ATP13A2	JHH6
+ATP6V0D2	SNU
+ATP8B1	JHH6
+ATP8B2	HUH
+ATP9B	JHH6
+AUTS2	HEP3B,SNU
+AXIN1	HEP3B
+AXIN2	HEP3B,HUH,JHH7,SNU
+AZGP1	HEP3B
+B3GALT1	SNU
+B3GALT2	HEP3B
+B3GNT9	HEP3B
+B4GALNT4	SNU
+BAAT	HEP3B
+BAGE2	JHH6
+BAIAP2L2	HEP3B
+BAMBI	JHH6
+BASP1	JHH6
+BAZ2B	HUH
+BBC3	SNU
+BCAM	SNU
+BCAN-AS1	HEP3B,JHH7
+BCHE	HEP3B
+BCL11A	HEP3B
+BCL2L14	HEP3B
+BCO2	HEP3B
+BCORL1	SNU
+BCYRN1	JHH6
+BDKRB2	HEP3B
+BDNF	HEP3B,SNU
+BEND7	SNU
+BEX4	SNU
+BHLHE41	HEP3B
+BHMT2	SNU
+BICC1	SNU
+BIK	HEP3B
+BIRC7	SNU
+BLNK	HUH
+BMF	SNU
+BMP1	HEP3B
+BMP2	JHH7
+BMP6	HUH
+BMP7	HEP3B
+BMPER	SNU
+bP-2189O9.5	HEP3B
+BRDT	HEP3B
+BTC	HEP3B,HUH
+BTG1	SNU
+BTG2	SNU
+C15orf48	SNU
+C1orf116	HUH,JHH6
+C1orf21	HEP3B
+C1orf94	SNU
+C1QL1	JHH6
+C1QTNF1	HEP3B
+C1S	HEP3B
+C22orf34	SNU
+C2orf15	SNU
+C3	HEP3B,HUH,JHH6,JHH7,SNU
+C3orf70	HEP3B
+C3P1	HUH
+C4A	HEP3B,SNU
+C4B	HEP3B,HUH,JHH7
+C4BPA	HEP3B,HUH
+C4BPB	JHH7
+C4orf54	SNU
+C6orf132	SNU
+C7	HUH,JHH6,JHH7,SNU
+C8orf58	JHH7
+C9orf116	SNU
+C9orf40	HEP3B
+CA11	HEP3B
+CA12	SNU
+CA5A	JHH7
+CACHD1	SNU
+CACNA1C	SNU
+CACNA1D	HUH
+CACNA1H	HEP3B
+CACNA2D1	SNU
+CACNA2D3	JHH6,JHH7
+CACNB4	JHH6
+CACNG4	JHH7
+CACNG7	SNU
+CADM4	SNU
+CALB2	SNU
+CALCOCO1	JHH7
+CALHM5	SNU
+CALN1	SNU
+CAMK1D	SNU
+CAMK2N1	HEP3B,SNU
+CAPN2	HEP3B
+CAPN6	JHH7
+CAPN8	JHH7
+CARD11	JHH6,SNU
+CARD16	JHH7,SNU
+CARD6	HEP3B
+CARMAL	HUH
+CARMIL1	SNU
+CARNS1	HEP3B
+CASC15	HEP3B
+CASC19	HEP3B
+CASP1	JHH7
+CAV1	HEP3B
+CAV2	HEP3B
+CAVIN3	JHH6
+CBR1	HEP3B
+CCDC141	JHH7
+CCDC144NL-AS1	HEP3B
+CCDC148	HEP3B
+CCDC198	JHH6
+CCDC24	HEP3B
+CCDC3	SNU
+CCDC69	SNU
+CCDC8	HEP3B,SNU
+CCDC80	HEP3B,SNU
+CCDC88C	SNU
+CCDC9B	HEP3B
+CCK	SNU
+CCKAR	SNU
+CCL2	JHH6,SNU
+CCN1	HEP3B,JHH7
+CCN2	HEP3B,JHH7
+CCN3	SNU
+CCN4	SNU
+CCNG2	JHH7
+CCR1	HUH,JHH7
+CCR3	SNU
+CCRL2	JHH6,SNU
+CD14	HEP3B
+CD163L1	HEP3B,JHH6,SNU
+CD24	JHH6
+CD302	JHH6
+CD33	HEP3B,SNU
+CD36	HEP3B
+CD37	SNU
+CD4	SNU
+CD44	SNU
+CD59	JHH7
+CD70	SNU
+CD82	HEP3B,HUH
+CD9	HEP3B,SNU
+CD96	SNU
+CDA	JHH6
+CDC42BPG	JHH6
+CDC42EP3	JHH7
+CDCA4	HEP3B
+CDH1	HEP3B,JHH6,JHH7
+CDH11	JHH7
+CDH16	HEP3B
+CDH19	HEP3B
+CDH23	HUH
+CDH6	SNU
+CDHR2	HEP3B
+CDIP1	SNU
+CDK18	JHH7
+CDKN1A	JHH6,JHH7
+CDKN2B	HEP3B
+CDO1	HEP3B
+CDS1	JHH6
+CEACAM6	JHH7
+CEBPA	JHH6
+CEMIP	SNU
+CENPV	HEP3B
+CEP112	HEP3B
+CERCAM	HUH
+CERS4	SNU
+CES1	HUH,SNU
+CES1P1	HUH
+CFAP221	HEP3B
+CFAP69	JHH7
+CFH	HEP3B,JHH6,SNU
+CFTR	HEP3B
+CGN	HEP3B
+CGREF1	SNU
+CH17-360D5.2	HEP3B,JHH7
+CH17-84K15.2	HEP3B
+CHAD	HEP3B
+CHI3L1	JHH6,SNU
+CHMP4C	JHH6
+CHN1	HEP3B
+CHPF2	HEP3B
+CHRM3	HEP3B
+CHRNA1	HEP3B
+CHST11	HUH
+CHST3	SNU
+CHST9	JHH6,JHH7
+CHSY1	HEP3B
+CIB2	SNU
+CIDEC	JHH7
+CITED2	HEP3B
+CKB	HEP3B
+CKMT2-AS1	SNU
+CLDN1	HEP3B,JHH6,SNU
+CLDN11	JHH6,SNU
+CLDN16	HEP3B
+CLDN2	JHH6,SNU
+CLDN3	SNU
+CLEC2B	SNU
+CLEC2L	HUH
+CLIC3	HEP3B
+CLIC5	HEP3B,JHH7
+CLIC6	JHH6
+CLIP3	SNU
+CLIP4	HEP3B
+CLSTN2	JHH6,SNU
+CLTB	HEP3B
+CLU	HUH
+CNIH3	HEP3B
+CNN1	HEP3B,JHH6,SNU
+CNNM1	SNU
+CNR1	SNU
+CNRIP1	JHH6
+CNTNAP1	SNU
+CNTNAP3	JHH6
+COBL	SNU
+COL21A1	SNU
+COL25A1	HEP3B
+COL26A1	HEP3B
+COL27A1	SNU
+COL2A1	HEP3B
+COL4A1	JHH7,SNU
+COL4A2	JHH7
+COL4A6	HEP3B,JHH6
+COL5A2	HEP3B
+COL6A1	HEP3B
+COL6A2	HEP3B
+COL7A1	HUH
+COL9A2	SNU
+COL9A3	HEP3B
+COLEC10	SNU
+COLEC11	HEP3B
+COPZ2	HEP3B
+CORIN	HEP3B
+CORO2A	JHH6
+CORO2B	JHH6
+CORO6	SNU
+CPA2	HEP3B
+CPA4	SNU
+CPEB4	HEP3B
+CPED1	HEP3B,SNU
+CPLANE1	HEP3B
+CPM	HEP3B
+CPN1	HEP3B
+CPN2	HEP3B
+CPNE2	HUH
+CPNE7	HUH
+CPS1	HEP3B
+CPT1A	HEP3B
+CPZ	SNU
+CRACDL	JHH6
+CREBRF	HEP3B
+CRIM1	HEP3B
+CRIP2	JHH6,SNU
+CRLF1	HEP3B,JHH7
+CRP	HEP3B
+CRYAB	HEP3B
+CRYL1	HEP3B
+CSAG1	HEP3B
+CSF1	SNU
+CSMD2	SNU
+CSPG4	SNU
+CTAG2	HEP3B
+CTB-25B13.12	HEP3B,JHH7
+CTB-63M22.1	JHH7,SNU
+CTB-92J24.3	SNU
+CTBP2	HEP3B
+CTC-308K20.1	HEP3B
+CTD-2003C8.2	SNU
+CTD-2062A1.3	HEP3B
+CTD-2091N23.1	SNU
+CTD-2201E18.8	HEP3B
+CTD-2297D10.2	SNU
+CTD-2334D19.1	SNU
+CTD-2396E7.11	JHH7
+CTD-2531D15.4	HEP3B
+CTD-2561J22.5	HEP3B
+CTD-2619J13.8	HEP3B
+CTD-3099C6.13	HEP3B
+CTD-3128G10.7	HEP3B,SNU
+CTDSPL	HEP3B
+CTNNA2	HEP3B
+CTNNAL1	HEP3B
+CTSF	HEP3B,SNU
+CTSO	HEP3B
+CTSS	HUH,JHH7,SNU
+CTSZ	JHH7
+CTTNBP2	HEP3B,SNU
+CTXN1	SNU
+CUBN	JHH6
+CX3CL1	HUH
+CXCL1	HEP3B,SNU
+CXCL12	HEP3B
+CXCL2	HEP3B
+CXCL5	HEP3B
+CXCL6	SNU
+CXCL8	SNU
+CXXC5	SNU
+CYB561	SNU
+CYFIP2	JHH7,SNU
+CYGB	HEP3B,SNU
+CYP1A1	SNU
+CYP2B6	HEP3B
+CYP2C9	SNU
+CYP2S1	HEP3B,SNU
+CYP2U1	JHH6
+CYP39A1	SNU
+CYP3A5	HUH
+CYSTM1	HEP3B
+DAAM2	HEP3B,SNU
+DAB1	HEP3B
+DAB2	HEP3B,SNU
+DAB2IP	SNU
+DACT2	HEP3B,SNU
+DAO	HEP3B
+DAPK3	JHH7
+DBNDD1	SNU
+DCBLD1	HEP3B
+DCHS1	SNU
+DCLK1	SNU
+DDC	HEP3B
+DDN	HEP3B
+DDO	JHH6
+DDX60	JHH7
+DDX60L	JHH7
+DEFB1	JHH7
+DENND1C	JHH7
+DENND6B	HEP3B
+DEPP1	HEP3B,HUH
+DEPTOR	HEP3B
+DGKB	SNU
+DGKG	HEP3B
+DHCR24	SNU
+DHRS2	JHH7
+DHX32	JHH7
+DIO2	SNU
+DIO3	SNU
+DIO3OS	SNU
+DIP2C	HEP3B,SNU
+DIP2C-AS1	HEP3B
+DIRAS1	HEP3B,SNU
+DIRC3	SNU
+DIRC3-AS1	SNU
+DISP2	HEP3B
+DLG3	JHH6
+DMBT1	SNU
+DMRT3	SNU
+DNAH11	SNU
+DNAH3	HEP3B
+DNAH5	HEP3B,HUH,SNU
+DNAJB9	HEP3B
+DNAJC6	HEP3B
+DNALI1	HEP3B
+DNASE1L1	SNU
+DNER	JHH6
+DNM1	SNU
+DNMT3B	HEP3B,HUH
+DOCK2	SNU
+DOCK4	SNU
+DOK1	SNU
+DOK7	HEP3B
+DPEP1	JHH7
+DPP4	HEP3B
+DPP7	SNU
+DPYSL3	JHH7
+DPYSL4	SNU
+DPYSL5	HEP3B
+DRAIC	HUH
+DSC2	SNU
+DSC3	SNU
+DSE	SNU
+DSP	HEP3B,JHH6
+DST	HEP3B
+DTNA	SNU
+DTX1	JHH6
+DTX3	SNU
+DUSP1	HEP3B,SNU
+DUSP13	HEP3B
+DUSP2	HEP3B
+DUSP8	HEP3B
+DUSP9	HEP3B
+DYNC1I1	HEP3B
+DYNC2H1	HEP3B
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+E2F7	HEP3B
+E2F8	HEP3B
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+EHD2	HEP3B
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+EIF5AL1	JHH7
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+ELF5	HEP3B
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+EPS8L1	HEP3B
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+FAM114A1	HEP3B
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+FAM13A	SNU
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+FAM167A	SNU
+FAM174B	HEP3B
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+FBXL2	HEP3B
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+FCHSD1	HEP3B
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+FGFR2	HEP3B
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+FOXC2	SNU
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+FREM1	HEP3B
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+G0S2	HEP3B
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+GADD45B	HEP3B
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+GALNT5	HEP3B
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+GAREM1	HEP3B
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+GBGT1	HEP3B
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+GCOM1	SNU
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+GJB7	HEP3B
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+GLT1D1	HUH
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+GLYATL1	HEP3B,JHH7
+GNAZ	SNU
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+GNG2	SNU
+GNG4	HEP3B
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+GOLGA8IP	HEP3B
+GP2	JHH7
+GPAM	HEP3B,SNU
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+GPR78	SNU
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+GPT	HEP3B,JHH6,JHH7,SNU
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+GUCY1B1	HEP3B
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+HORMAD2	HEP3B
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+HOXA11	HUH
+HOXA3	HEP3B
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+HOXB9	SNU
+HOXC13	HEP3B
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+HS3ST1	HEP3B
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+KIAA1755	SNU
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+KPNA7	SNU
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+LINC01980	HEP3B
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+OSBP2	SNU
+OSBPL10	HUH
+OSBPL5	SNU
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diff -r 000000000000 -r f005c350af7f upset.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/upset.R	Sat Dec 17 16:53:08 2022 +0000
@@ -0,0 +1,45 @@
+library(tidyverse)
+library(ggupset)
+
+args <- commandArgs(trailingOnly = TRUE)
+n_int <- as.integer(args[1])
+x_lab <- as.character(args[2])
+y_lab <- as.character(args[3])
+width <- as.integer(args[4])
+height <- as.integer(args[5])
+files <- tail(args, -5)
+
+# gene, (list of matching conditions)
+data <- list()
+for (idx in seq_along(files)) {
+  k <- files[idx]
+  data[k] <- read_tsv(k, col_names = c("genes"))
+}
+
+all_genes <- c()
+for (gene_list in data){
+  for (gene in gene_list){
+    all_genes <- append(all_genes, gene)
+  }
+}
+all_genes <- unique(sort(all_genes))
+
+trans <- tibble(gene = character(), files = character())
+for (gene_idx in seq_along(all_genes)) {
+  gene <- all_genes[gene_idx]
+  files <- names(data)[grep(gene, data)]
+  files <- paste(files, sep = ",", collapse = ",")
+  trans <- trans %>% add_row(gene = gene, files = files)
+}
+
+write_tsv(trans, "upset.tsv")
+trans$f <- str_split(trans$files, ",")
+
+pl <- trans %>% ggplot(aes(x = f)) + geom_bar() +
+    scale_x_upset(n_intersections = n_int, order_by = "freq") +
+    xlab(x_lab) + ylab(y_lab)
+ggsave("upset-freq.png", width = width, height = height, units = "px")
+pl <- trans %>% ggplot(aes(x = f)) + geom_bar() +
+    scale_x_upset(n_intersections = n_int, order_by = "degree") +
+    xlab(x_lab) + ylab(y_lab)
+ggsave("upset-degree.png", width = width, height = height, units = "px")