fix vignette build

vignettes/GOeval.Rmd

@@ -65,7 +65,7 @@ out_dir <- "data"
 
 Run the `evaluate` function.
 
-```{r}
+```{r, eval = FALSE}
 net_1_data <- evaluate(network_path, reference_path, out_dir, network_name,
                       # some additional arguments
                       edges = c(512, 1024, 2048, 3174, 4096, 8192, 16384, 32768, 65536),
@@ -83,7 +83,7 @@ The run time of the evaluate function changes with the size of the network and t
 
 Now, let us compare with a second network. The "small_dto.tsv" network does not have edge scores, so no network subsets will be created. Generate the data for this network in a similar way as for the first one.
 
-```{r}
+```{r, eval = FALSE}
 net_2_data <- evaluate(file.path(data_dir, "small_dto.tsv"),
                        file.path(data_dir, "h1_k562_overlap_universe.txt"),
                        out_dir,
@@ -96,6 +96,12 @@ net_2_data <- evaluate(file.path(data_dir, "small_dto.tsv"),
 
 Use the output from both networks in the call to `plot_metrics`.
 
+```{r, echo = FALSE}
+net_1_data <- list(get_metrics(file.path(data_dir, "np3_summaries"), get_annotation_overlap = TRUE))
+
+net_2_data <- list(get_metrics(file.path(data_dir, "dto_summaries"), get_annotation_overlap = TRUE))
+```
+
 ```{r}
 # set main plot titles
 title_text <- "NP3 vs DTO"

vignettes/data/dto_summaries/dto_3174/p1/ENSG00000068305_ORA_summary.csv

@@ -1,17 +1,17 @@
 "geneSet","description","size","overlap","expect","enrichmentRatio","pValue","FDR","overlapId","userId","database"
-"GO:0097193","intrinsic apoptotic signaling pathway",233,2,0.0774429426102371,25.8254649499285,0.00195680321876113,1,"6648;64782","ENSG00000112096;ENSG00000181026","geneontology_Biological_Process_noRedundant"
-"GO:0070671","response to interleukin-12",38,1,0.0126301794814979,79.1754385964912,0.0125784681009865,1,"6648","ENSG00000112096","geneontology_Biological_Process_noRedundant"
-"GO:0010657","muscle cell apoptotic process",43,1,0.0142920452027476,69.968992248062,0.0142256344761132,1,"6648","ENSG00000112096","geneontology_Biological_Process_noRedundant"
-"GO:0051262","protein tetramerization",92,1,0.0305783292709949,32.7028985507246,0.03027102985761,1,"6648","ENSG00000112096","geneontology_Biological_Process_noRedundant"
-"GO:0008637","apoptotic mitochondrial changes",96,1,0.0319078218479947,31.3402777777778,0.0315731162606272,1,"6648","ENSG00000112096","geneontology_Biological_Process_noRedundant"
-"GO:0033002","muscle cell proliferation",98,1,0.0325725681364946,30.7006802721088,0.0322237221453761,1,"6648","ENSG00000112096","geneontology_Biological_Process_noRedundant"
-"GO:0010821","regulation of mitochondrion organization",150,1,0.0498559716374917,20.0577777777778,0.0490373645829694,1,"80821","ENSG00000100523","geneontology_Biological_Process_noRedundant"
-"GO:0072593","reactive oxygen species metabolic process",152,1,0.0505207179259916,19.7938596491228,0.0496801240363475,1,"6648","ENSG00000112096","geneontology_Biological_Process_noRedundant"
-"GO:1901342","regulation of vasculature development",164,1,0.0545091956569909,18.3455284552846,0.0535305994596911,1,"6648","ENSG00000112096","geneontology_Biological_Process_noRedundant"
-"GO:0016042","lipid catabolic process",185,1,0.0614890316862398,16.2630630630631,0.0602438790965963,1,"80821","ENSG00000100523","geneontology_Biological_Process_noRedundant"
-"GO:0042692","muscle cell differentiation",187,1,0.0621537779747396,16.0891265597148,0.0608815783254052,1,"6648","ENSG00000112096","geneontology_Biological_Process_noRedundant"
-"GO:0072331","signal transduction by p53 class mediator",192,1,0.0638156436959894,15.6701388888889,0.0624745641266515,1,"64782","ENSG00000181026","geneontology_Biological_Process_noRedundant"
-"GO:0051260","protein homooligomerization",201,1,0.0668070019942389,14.9684908789386,0.0653373971366136,1,"6648","ENSG00000112096","geneontology_Biological_Process_noRedundant"
-"GO:0007568","aging",202,1,0.0671393751384888,14.8943894389439,0.0656551294661987,1,"6648","ENSG00000112096","geneontology_Biological_Process_noRedundant"
-"GO:0003013","circulatory system process",208,1,0.0691336140039885,14.4647435897436,0.0675600114041581,1,"6648","ENSG00000112096","geneontology_Biological_Process_noRedundant"
-"GO:0070997","neuron death",227,1,0.0754487037447374,13.2540381791483,0.0735750538943237,1,"6648","ENSG00000112096","geneontology_Biological_Process_noRedundant"
+"GO:0097485","neuron projection guidance",141,2,0.156215377797474,12.8028368794326,0.0100440485712068,1,"2115;6712","ENSG00000173898;ENSG00000006468","geneontology_Biological_Process_noRedundant"
+"GO:0031579","membrane raft organization",13,1,0.0144028362508309,69.4307692307692,0.014316938201237,1,"2319","ENSG00000132589","geneontology_Biological_Process_noRedundant"
+"GO:0044091","membrane biogenesis",21,1,0.0232661200974961,42.9809523809524,0.0230354015441375,1,"2319","ENSG00000132589","geneontology_Biological_Process_noRedundant"
+"GO:0034113","heterotypic cell-cell adhesion",22,1,0.0243740305783293,41.0272727272727,0.0241203150349263,1,"2319","ENSG00000132589","geneontology_Biological_Process_noRedundant"
+"GO:0072348","sulfur compound transport",28,1,0.0310214934633282,32.2357142857143,0.030607056618129,1,"65010","ENSG00000225697","geneontology_Biological_Process_noRedundant"
+"GO:0007586","digestion",35,1,0.0387768668291602,25.7885714285714,0.0381258571546177,1,"65010","ENSG00000225697","geneontology_Biological_Process_noRedundant"
+"GO:0061564","axon development",296,2,0.327941502326612,6.09864864864865,0.0405343828762099,1,"2115;6712","ENSG00000173898;ENSG00000006468","geneontology_Biological_Process_noRedundant"
+"GO:0045445","myoblast differentiation",38,1,0.0421005982716596,23.7526315789474,0.0413321016805785,1,"2319","ENSG00000132589","geneontology_Biological_Process_noRedundant"
+"GO:0070671","response to interleukin-12",38,1,0.0421005982716596,23.7526315789474,0.0413321016805785,1,"6627","ENSG00000131876","geneontology_Biological_Process_noRedundant"
+"GO:0042982","amyloid precursor protein metabolic process",39,1,0.0432085087524928,23.1435897435897,0.0423987103791986,1,"2319","ENSG00000132589","geneontology_Biological_Process_noRedundant"
+"GO:0046717","acid secretion",40,1,0.0443164192333259,22.565,0.0434642509262342,1,"65010","ENSG00000225697","geneontology_Biological_Process_noRedundant"
+"GO:0099072","regulation of postsynaptic membrane neurotransmitter receptor levels",40,1,0.0443164192333259,22.565,0.0434642509262342,1,"2319","ENSG00000132589","geneontology_Biological_Process_noRedundant"
+"GO:0007422","peripheral nervous system development",41,1,0.0454243297141591,22.0146341463415,0.0445287242726327,1,"2115","ENSG00000006468","geneontology_Biological_Process_noRedundant"
+"GO:0048193","Golgi vesicle transport",315,2,0.348991801462442,5.73079365079365,0.0454008207684142,1,"6712;22796","ENSG00000173898;ENSG00000135775","geneontology_Biological_Process_noRedundant"
+"GO:0043631","RNA polyadenylation",46,1,0.0509638821183248,19.6217391304348,0.0498351162263958,1,"10914","ENSG00000090060","geneontology_Biological_Process_noRedundant"
+"GO:0030534","adult behavior",59,1,0.0653667183691558,15.2983050847458,0.06350783285485,1,"6712","ENSG00000173898","geneontology_Biological_Process_noRedundant"

vignettes/data/dto_summaries/dto_3174/p1/ENSG00000068323_ORA_summary.csv

@@ -1,17 +1,17 @@
 "geneSet","description","size","overlap","expect","enrichmentRatio","pValue","FDR","overlapId","userId","database"
-"GO:0045926","negative regulation of growth",142,7,1.77775315754487,3.93755453072417,0.00198386094076897,1,"604;4501;8614;10500;10501;83667;84260","ENSG00000139437;ENSG00000113739;ENSG00000167680;ENSG00000143434;ENSG00000113916;ENSG00000187193;ENSG00000130766","geneontology_Biological_Process_noRedundant"
-"GO:0035270","endocrine system development",56,4,0.701085752271217,5.70543615676359,0.00518631353762666,1,"2932;3570;5170;5307","ENSG00000069011;ENSG00000160712;ENSG00000082701;ENSG00000140992","geneontology_Biological_Process_noRedundant"
-"GO:0061448","connective tissue development",137,6,1.7151562153778,3.49822362896454,0.00735010076279985,1,"864;1292;4781;5307;5916;91461","ENSG00000069011;ENSG00000172819;ENSG00000142173;ENSG00000020633;ENSG00000162878;ENSG00000147862","geneontology_Biological_Process_noRedundant"
-"GO:0061564","axon development",296,9,3.70573897629072,2.42866539105477,0.0117824327410532,1,"2932;4548;4781;6812;9260;10500;10501;51199;57463","ENSG00000196923;ENSG00000167680;ENSG00000143434;ENSG00000082701;ENSG00000136854;ENSG00000100503;ENSG00000181754;ENSG00000147862;ENSG00000116984","geneontology_Biological_Process_noRedundant"
-"GO:0009187","cyclic nucleotide metabolic process",14,2,0.175271438067804,11.4108723135272,0.012814735869088,1,"5141;5151","ENSG00000065989;ENSG00000073417","geneontology_Biological_Process_noRedundant"
-"GO:0031016","pancreas development",40,3,0.500775537336583,5.99070796460177,0.0134861965849173,1,"2932;3570;5170","ENSG00000160712;ENSG00000082701;ENSG00000140992","geneontology_Biological_Process_noRedundant"
-"GO:0007272","ensheathment of neurons",74,4,0.926434744072679,4.31762736187515,0.0136917221851089,1,"4664;5916;8506;57463","ENSG00000108797;ENSG00000172819;ENSG00000138386;ENSG00000181754","geneontology_Biological_Process_noRedundant"
-"GO:0016049","cell growth",305,9,3.81841347219145,2.35699985492529,0.0141130576883431,1,"604;2932;5916;10500;10501;51199;83452;83667;84260","ENSG00000139437;ENSG00000172819;ENSG00000167680;ENSG00000143434;ENSG00000082701;ENSG00000113916;ENSG00000172007;ENSG00000100503;ENSG00000130766","geneontology_Biological_Process_noRedundant"
-"GO:0032102","negative regulation of response to external stimulus",158,6,1.9780633724795,3.03326985549457,0.0142314505592482,1,"4846;10500;10501;22900;26146;29937","ENSG00000117691;ENSG00000167680;ENSG00000143434;ENSG00000105483;ENSG00000164867;ENSG00000204104","geneontology_Biological_Process_noRedundant"
-"GO:0007422","peripheral nervous system development",41,3,0.513294925769998,5.84459313619685,0.0144205812972097,1,"864;4664;8506","ENSG00000108797;ENSG00000138386;ENSG00000020633","geneontology_Biological_Process_noRedundant"
-"GO:0032886","regulation of microtubule-based process",167,6,2.09073786838023,2.86980022256372,0.018236402755863,1,"1729;2932;26146;51199;79648;255758","ENSG00000082701;ENSG00000213123;ENSG00000147316;ENSG00000100503;ENSG00000131504;ENSG00000204104","geneontology_Biological_Process_noRedundant"
-"GO:0010737","protein kinase A signaling",17,2,0.212829603368048,9.39718896408121,0.0186901982200889,1,"5141;9495","ENSG00000065989;ENSG00000179841","geneontology_Biological_Process_noRedundant"
-"GO:0010959","regulation of metal ion transport",174,6,2.17837358741414,2.75434848947208,0.0218426963362333,1,"1729;4846;5170;7779;8614;57463","ENSG00000113739;ENSG00000140992;ENSG00000131504;ENSG00000170385;ENSG00000181754;ENSG00000164867","geneontology_Biological_Process_noRedundant"
-"GO:0044380","protein localization to cytoskeleton",50,3,0.625969421670729,4.79256637168142,0.0244582145633063,1,"1729;2932;79648","ENSG00000082701;ENSG00000147316;ENSG00000131504","geneontology_Biological_Process_noRedundant"
-"GO:0001818","negative regulation of cytokine production",133,5,1.66507866164414,3.00286113513873,0.0255327078073819,1,"604;8986;9246;22900;26146","ENSG00000113916;ENSG00000162302;ENSG00000105483;ENSG00000204104;ENSG00000156587","geneontology_Biological_Process_noRedundant"
-"GO:0060560","developmental growth involved in morphogenesis",133,5,1.66507866164414,3.00286113513873,0.0255327078073819,1,"2932;5916;10500;10501;51199","ENSG00000172819;ENSG00000167680;ENSG00000143434;ENSG00000082701;ENSG00000100503","geneontology_Biological_Process_noRedundant"
+"GO:0007398","ectoderm development",12,1,0.011965433192998,83.5740740740741,0.0119072481758324,1,"8324","ENSG00000155760","geneontology_Biological_Process_noRedundant"
+"GO:0018200","peptidyl-glutamic acid modification",17,1,0.0169510303567472,58.9934640522876,0.0168312887479818,1,"79739","ENSG00000137941","geneontology_Biological_Process_noRedundant"
+"GO:0042110","T cell activation",232,2,0.231331708397961,8.6455938697318,0.0210227670583794,1,"896;8324","ENSG00000155760;ENSG00000112576","geneontology_Biological_Process_noRedundant"
+"GO:0017145","stem cell division",27,1,0.0269222246842455,37.1440329218107,0.0266139826801229,1,"8324","ENSG00000155760","geneontology_Biological_Process_noRedundant"
+"GO:0007164","establishment of tissue polarity",53,1,0.0528473299357412,18.9224318658281,0.0516452814443892,1,"8324","ENSG00000155760","geneontology_Biological_Process_noRedundant"
+"GO:0006360","transcription by RNA polymerase I",60,1,0.05982716596499,16.7148148148148,0.0582859516953478,1,"7343","ENSG00000108312","geneontology_Biological_Process_noRedundant"
+"GO:0035051","cardiocyte differentiation",65,1,0.0648127631287392,15.4290598290598,0.0630039485689942,1,"8324","ENSG00000155760","geneontology_Biological_Process_noRedundant"
+"GO:0045995","regulation of embryonic development",71,1,0.0707954797252382,14.1251956181534,0.0686378022561223,1,"8324","ENSG00000155760","geneontology_Biological_Process_noRedundant"
+"GO:0006353","DNA-templated transcription, termination",73,1,0.0727897185907379,13.738203957382,0.0705090507635261,1,"7343","ENSG00000108312","geneontology_Biological_Process_noRedundant"
+"GO:1904029","regulation of cyclin-dependent protein kinase activity",77,1,0.0767781963217372,13.024531024531,0.0742415251031704,1,"896","ENSG00000112576","geneontology_Biological_Process_noRedundant"
+"GO:0007369","gastrulation",91,1,0.0907378683802349,11.020757020757,0.0872004944407176,1,"8324","ENSG00000155760","geneontology_Biological_Process_noRedundant"
+"GO:0045165","cell fate commitment",98,1,0.0977177044094837,10.2335600907029,0.0936193066711634,1,"8324","ENSG00000155760","geneontology_Biological_Process_noRedundant"
+"GO:0098727","maintenance of cell number",98,1,0.0977177044094837,10.2335600907029,0.0936193066711634,1,"8324","ENSG00000155760","geneontology_Biological_Process_noRedundant"
+"GO:2000027","regulation of animal organ morphogenesis",100,1,0.0997119432749834,10.0288888888889,0.0954458682907182,1,"8324","ENSG00000155760","geneontology_Biological_Process_noRedundant"
+"GO:0031099","regeneration",104,1,0.103700421005983,9.64316239316239,0.0990891786394831,1,"8324","ENSG00000155760","geneontology_Biological_Process_noRedundant"
+"GO:0007219","Notch signaling pathway",117,1,0.116662973631731,8.57169990503324,0.11084002471008,1,"142678","ENSG00000197530","geneontology_Biological_Process_noRedundant"