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tests/testthat/_snaps/netwokHelpers.md
In ingres: Infer Gene Probabilistic Boolean Networks from Single-Cell Data
createNetworkGenesTemplate correctly returns the template file
Code
createNetworkGenesTemplate(network, store = F, modify = F)
Output
# A tibble: 25 x 2
node symbol
<chr> <chr>
1 EGFR EGFR
2 FGFR3 FGFR3
3 RAS RAS
4 E2F1_1 E2F1_1
5 E2F1_2 E2F1_2
6 E2F3_1 E2F3_1
7 E2F3_2 E2F3_2
8 CyclinD1 CyclinD1
9 CyclinE1 CyclinE1
10 CyclinA CyclinA
# ... with 15 more rows
ginmlToGraphml correctly returns a graphml file as a vector
Code
ginmlToGraphml(system.file("extdata", "example_ginsim.zginml", package = "ingres"),
dest = withr::local_tempfile(fileext = ".graphml"))
Output
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?><graphml xmlns=\"http://graphml.graphdrawing.org/xmlns\">"
[2] "<key attr.name=\"kind\" attr.type=\"string\" for=\"node\" id=\"kind\"/>"
[3] "<key attr.name=\"rule\" attr.type=\"string\" for=\"node\" id=\"rule\"/>"
[4] "<key attr.name=\"sign\" attr.type=\"string\" for=\"edge\" id=\"sign\"/>"
[5] "<graph edgedefault=\"directed\">"
[6] "<node id=\"DNA_Damage\">"
[7] "<data key=\"kind\">input</data>"
[8] "</node>"
[9] "<node id=\"ATM\">"
[10] "<data key=\"rule\">DNA_Damage and (E2F1 or not Wip1 or not HDAC1)</data>"
[11] "<data key=\"kind\">gene</data>"
[12] "</node>"
[13] "<node id=\"p38MAPK\">"
[14] "<data key=\"rule\">ATM and not Wip1</data>"
[15] "<data key=\"kind\">gene</data>"
[16] "</node>"
[17] "<node id=\"Mdm2\">"
[18] "<data key=\"rule\">(not Wip1 or p53) and not ATM</data>"
[19] "<data key=\"kind\">gene</data>"
[20] "</node>"
[21] "<node id=\"p53\">"
[22] "<data key=\"rule\">ATM or (not Mdm2 and p38MAPK)</data>"
[23] "<data key=\"kind\">gene</data>"
[24] "</node>"
[25] "<node id=\"Wip1\">"
[26] "<data key=\"rule\">p53_A</data>"
[27] "<data key=\"kind\">gene</data>"
[28] "</node>"
[29] "<node id=\"p53_A\">"
[30] "<data key=\"rule\">not Sirt_1 and not p53_K and (p53:1 or not p53_INP1)</data>"
[31] "<data key=\"kind\">gene</data>"
[32] "</node>"
[33] "<node id=\"p53_K\">"
[34] "<data key=\"rule\">not p53_A and (not Sirt_1 or not Wip1) and p53</data>"
[35] "<data key=\"kind\">gene</data>"
[36] "</node>"
[37] "<node id=\"miR_34a\">"
[38] "<data key=\"rule\">ATM</data>"
[39] "<data key=\"kind\">gene</data>"
[40] "</node>"
[41] "<node id=\"p21\">"
[42] "<data key=\"rule\">p53_A or ((not HDAC1 or not c_Myc) and not Caspase3 and p38MAPK)</data>"
[43] "<data key=\"kind\">gene</data>"
[44] "</node>"
[45] "<node id=\"p53_INP1\">"
[46] "<data key=\"rule\">p53_K or p53_A</data>"
[47] "<data key=\"kind\">gene</data>"
[48] "</node>"
[49] "<node id=\"c_Myc\">"
[50] "<data key=\"rule\">(E2F1 or p38MAPK or not miR_34a) and not RB and not p21</data>"
[51] "<data key=\"kind\">gene</data>"
[52] "</node>"
[53] "<node id=\"Cdc25A\">"
[54] "<data key=\"rule\">(not ATM and not miR_34a) or not p38MAPK</data>"
[55] "<data key=\"kind\">gene</data>"
[56] "</node>"
[57] "<node id=\"cdk46_CycD\">"
[58] "<data key=\"rule\">Cdc25A and not miR_34a and not p21</data>"
[59] "<data key=\"kind\">gene</data>"
[60] "</node>"
[61] "<node id=\"cdk2_CycE\">"
[62] "<data key=\"rule\">Cdc25A and E2F1 and not miR_34a and not p21</data>"
[63] "<data key=\"kind\">gene</data>"
[64] "</node>"
[65] "<node id=\"RB\">"
[66] "<data key=\"rule\">not cdk46_CycD and not cdk2_CycE</data>"
[67] "<data key=\"kind\">gene</data>"
[68] "</node>"
[69] "<node id=\"E2F1\">"
[70] "<data key=\"rule\">(not RB and ((Cdc25A and ATM) or not Sirt_1 or not miR_34a)) or c_Myc</data>"
[71] "<data key=\"kind\">gene</data>"
[72] "</node>"
[73] "<node id=\"Sirt_1\">"
[74] "<data key=\"rule\">E2F1 and not (HDAC1 and miR_34a)</data>"
[75] "<data key=\"kind\">gene</data>"
[76] "</node>"
[77] "<node id=\"HDAC1\">"
[78] "<data key=\"rule\">(not miR_34a and not Sirt_1) or not DNA_Damage</data>"
[79] "<data key=\"kind\">gene</data>"
[80] "</node>"
[81] "<node id=\"PUMA\">"
[82] "<data key=\"rule\">p53_K</data>"
[83] "<data key=\"kind\">gene</data>"
[84] "</node>"
[85] "<node id=\"BCL2\">"
[86] "<data key=\"rule\">not PUMA and not miR_34a</data>"
[87] "<data key=\"kind\">gene</data>"
[88] "</node>"
[89] "<node id=\"BAX\">"
[90] "<data key=\"rule\">not BCL2 and p53_K</data>"
[91] "<data key=\"kind\">gene</data>"
[92] "</node>"
[93] "<node id=\"Caspase3\">"
[94] "<data key=\"rule\">not (BCL2 and p21) and BAX</data>"
[95] "<data key=\"kind\">gene</data>"
[96] "</node>"
[97] "<node id=\"Proliferation\">"
[98] "<data key=\"rule\">E2F1 and not p53</data>"
[99] "<data key=\"kind\">gene</data>"
[100] "</node>"
[101] "<node id=\"SIPS\">"
[102] "<data key=\"rule\">p21 and not E2F1</data>"
[103] "<data key=\"kind\">gene</data>"
[104] "</node>"
[105] "<node id=\"Apoptosis\">"
[106] "<data key=\"rule\">Caspase3</data>"
[107] "<data key=\"kind\">gene</data>"
[108] "</node>"
[109] "<edge source=\"Sirt_1\" target=\"p53_K\">"
[110] "<data key=\"sign\">negative</data>"
[111] "</edge>"
[112] "<edge source=\"Sirt_1\" target=\"p53_A\">"
[113] "<data key=\"sign\">negative</data>"
[114] "</edge>"
[115] "<edge source=\"Sirt_1\" target=\"E2F1\">"
[116] "<data key=\"sign\">negative</data>"
[117] "</edge>"
[118] "<edge source=\"Sirt_1\" target=\"HDAC1\">"
[119] "<data key=\"sign\">negative</data>"
[120] "</edge>"
[121] "<edge source=\"p53_INP1\" target=\"p53_A\">"
[122] "<data key=\"sign\">negative</data>"
[123] "</edge>"
[124] "<edge source=\"p53_A\" target=\"p53_K\">"
[125] "<data key=\"sign\">negative</data>"
[126] "</edge>"
[127] "<edge source=\"p53_A\" target=\"p21\">"
[128] "<data key=\"sign\">positive</data>"
[129] "</edge>"
[130] "<edge source=\"p53_A\" target=\"Wip1\">"
[131] "<data key=\"sign\">positive</data>"
[132] "</edge>"
[133] "<edge source=\"p53_A\" target=\"p53_INP1\">"
[134] "<data key=\"sign\">positive</data>"
[135] "</edge>"
[136] "<edge source=\"Mdm2\" target=\"p53\">"
[137] "<data key=\"sign\">negative</data>"
[138] "</edge>"
[139] "<edge source=\"Wip1\" target=\"ATM\">"
[140] "<data key=\"sign\">negative</data>"
[141] "</edge>"
[142] "<edge source=\"Wip1\" target=\"Mdm2\">"
[143] "<data key=\"sign\">negative</data>"
[144] "</edge>"
[145] "<edge source=\"Wip1\" target=\"p53_K\">"
[146] "<data key=\"sign\">negative</data>"
[147] "</edge>"
[148] "<edge source=\"Wip1\" target=\"p38MAPK\">"
[149] "<data key=\"sign\">negative</data>"
[150] "</edge>"
[151] "<edge source=\"p53_K\" target=\"p53_A\">"
[152] "<data key=\"sign\">negative</data>"
[153] "</edge>"
[154] "<edge source=\"p53_K\" target=\"p53_INP1\">"
[155] "<data key=\"sign\">positive</data>"
[156] "</edge>"
[157] "<edge source=\"p53_K\" target=\"BAX\">"
[158] "<data key=\"sign\">positive</data>"
[159] "</edge>"
[160] "<edge source=\"p53_K\" target=\"PUMA\">"
[161] "<data key=\"sign\">positive</data>"
[162] "</edge>"
[163] "<edge source=\"E2F1\" target=\"Sirt_1\">"
[164] "<data key=\"sign\">positive</data>"
[165] "</edge>"
[166] "<edge source=\"E2F1\" target=\"ATM\">"
[167] "<data key=\"sign\">positive</data>"
[168] "</edge>"
[169] "<edge source=\"E2F1\" target=\"c_Myc\">"
[170] "<data key=\"sign\">positive</data>"
[171] "</edge>"
[172] "<edge source=\"E2F1\" target=\"cdk2_CycE\">"
[173] "<data key=\"sign\">positive</data>"
[174] "</edge>"
[175] "<edge source=\"E2F1\" target=\"Proliferation\">"
[176] "<data key=\"sign\">positive</data>"
[177] "</edge>"
[178] "<edge source=\"E2F1\" target=\"SIPS\">"
[179] "<data key=\"sign\">negative</data>"
[180] "</edge>"
[181] "<edge source=\"cdk2_CycE\" target=\"RB\">"
[182] "<data key=\"sign\">negative</data>"
[183] "</edge>"
[184] "<edge source=\"ATM\" target=\"p53\">"
[185] "<data key=\"sign\">positive</data>"
[186] "</edge>"
[187] "<edge source=\"ATM\" target=\"Mdm2\">"
[188] "<data key=\"sign\">negative</data>"
[189] "</edge>"
[190] "<edge source=\"ATM\" target=\"E2F1\">"
[191] "<data key=\"sign\">positive</data>"
[192] "</edge>"
[193] "<edge source=\"ATM\" target=\"Cdc25A\">"
[194] "<data key=\"sign\">negative</data>"
[195] "</edge>"
[196] "<edge source=\"ATM\" target=\"p38MAPK\">"
[197] "<data key=\"sign\">positive</data>"
[198] "</edge>"
[199] "<edge source=\"ATM\" target=\"miR_34a\">"
[200] "<data key=\"sign\">positive</data>"
[201] "</edge>"
[202] "<edge source=\"p38MAPK\" target=\"p53\">"
[203] "<data key=\"sign\">positive</data>"
[204] "</edge>"
[205] "<edge source=\"p38MAPK\" target=\"c_Myc\">"
[206] "<data key=\"sign\">positive</data>"
[207] "</edge>"
[208] "<edge source=\"p38MAPK\" target=\"p21\">"
[209] "<data key=\"sign\">positive</data>"
[210] "</edge>"
[211] "<edge source=\"p38MAPK\" target=\"Cdc25A\">"
[212] "<data key=\"sign\">negative</data>"
[213] "</edge>"
[214] "<edge source=\"PUMA\" target=\"BCL2\">"
[215] "<data key=\"sign\">negative</data>"
[216] "</edge>"
[217] "<edge source=\"p21\" target=\"cdk46_CycD\">"
[218] "<data key=\"sign\">negative</data>"
[219] "</edge>"
[220] "<edge source=\"p21\" target=\"c_Myc\">"
[221] "<data key=\"sign\">negative</data>"
[222] "</edge>"
[223] "<edge source=\"p21\" target=\"Caspase3\">"
[224] "<data key=\"sign\">negative</data>"
[225] "</edge>"
[226] "<edge source=\"p21\" target=\"cdk2_CycE\">"
[227] "<data key=\"sign\">negative</data>"
[228] "</edge>"
[229] "<edge source=\"p21\" target=\"SIPS\">"
[230] "<data key=\"sign\">positive</data>"
[231] "</edge>"
[232] "<edge source=\"miR_34a\" target=\"HDAC1\">"
[233] "<data key=\"sign\">negative</data>"
[234] "</edge>"
[235] "<edge source=\"miR_34a\" target=\"E2F1\">"
[236] "<data key=\"sign\">negative</data>"
[237] "</edge>"
[238] "<edge source=\"miR_34a\" target=\"Sirt_1\">"
[239] "<data key=\"sign\">negative</data>"
[240] "</edge>"
[241] "<edge source=\"miR_34a\" target=\"BCL2\">"
[242] "<data key=\"sign\">negative</data>"
[243] "</edge>"
[244] "<edge source=\"miR_34a\" target=\"cdk46_CycD\">"
[245] "<data key=\"sign\">negative</data>"
[246] "</edge>"
[247] "<edge source=\"miR_34a\" target=\"cdk2_CycE\">"
[248] "<data key=\"sign\">negative</data>"
[249] "</edge>"
[250] "<edge source=\"miR_34a\" target=\"c_Myc\">"
[251] "<data key=\"sign\">negative</data>"
[252] "</edge>"
[253] "<edge source=\"miR_34a\" target=\"Cdc25A\">"
[254] "<data key=\"sign\">negative</data>"
[255] "</edge>"
[256] "<edge source=\"c_Myc\" target=\"p21\">"
[257] "<data key=\"sign\">negative</data>"
[258] "</edge>"
[259] "<edge source=\"c_Myc\" target=\"E2F1\">"
[260] "<data key=\"sign\">positive</data>"
[261] "</edge>"
[262] "<edge source=\"DNA_Damage\" target=\"ATM\">"
[263] "<data key=\"sign\">positive</data>"
[264] "</edge>"
[265] "<edge source=\"DNA_Damage\" target=\"HDAC1\">"
[266] "<data key=\"sign\">negative</data>"
[267] "</edge>"
[268] "<edge source=\"Caspase3\" target=\"p21\">"
[269] "<data key=\"sign\">negative</data>"
[270] "</edge>"
[271] "<edge source=\"Caspase3\" target=\"Apoptosis\">"
[272] "<data key=\"sign\">positive</data>"
[273] "</edge>"
[274] "<edge source=\"HDAC1\" target=\"p21\">"
[275] "<data key=\"sign\">negative</data>"
[276] "</edge>"
[277] "<edge source=\"HDAC1\" target=\"Sirt_1\">"
[278] "<data key=\"sign\">negative</data>"
[279] "</edge>"
[280] "<edge source=\"HDAC1\" target=\"ATM\">"
[281] "<data key=\"sign\">negative</data>"
[282] "</edge>"
[283] "<edge source=\"RB\" target=\"E2F1\">"
[284] "<data key=\"sign\">negative</data>"
[285] "</edge>"
[286] "<edge source=\"RB\" target=\"c_Myc\">"
[287] "<data key=\"sign\">negative</data>"
[288] "</edge>"
[289] "<edge source=\"p53\" target=\"p53_A\">"
[290] "<data key=\"sign\">positive</data>"
[291] "</edge>"
[292] "<edge source=\"p53\" target=\"Mdm2\">"
[293] "<data key=\"sign\">positive</data>"
[294] "</edge>"
[295] "<edge source=\"p53\" target=\"p53_K\">"
[296] "<data key=\"sign\">positive</data>"
[297] "</edge>"
[298] "<edge source=\"p53\" target=\"Proliferation\">"
[299] "<data key=\"sign\">negative</data>"
[300] "</edge>"
[301] "<edge source=\"Cdc25A\" target=\"E2F1\">"
[302] "<data key=\"sign\">positive</data>"
[303] "</edge>"
[304] "<edge source=\"Cdc25A\" target=\"cdk46_CycD\">"
[305] "<data key=\"sign\">positive</data>"
[306] "</edge>"
[307] "<edge source=\"Cdc25A\" target=\"cdk2_CycE\">"
[308] "<data key=\"sign\">positive</data>"
[309] "</edge>"
[310] "<edge source=\"cdk46_CycD\" target=\"RB\">"
[311] "<data key=\"sign\">negative</data>"
[312] "</edge>"
[313] "<edge source=\"BCL2\" target=\"BAX\">"
[314] "<data key=\"sign\">negative</data>"
[315] "</edge>"
[316] "<edge source=\"BCL2\" target=\"Caspase3\">"
[317] "<data key=\"sign\">negative</data>"
[318] "</edge>"
[319] "<edge source=\"BAX\" target=\"Caspase3\">"
[320] "<data key=\"sign\">positive</data>"
[321] "</edge>"
[322] "</graph>"
[323] "</graphml>"
printAllNodes correctly prints a network
Code
printAllNodes(network)
Output
# A tibble: 30 x 3
kind rule id
<chr> <chr> <chr>
1 input "" DNAd~
2 input "" Grow~
3 fate "CyclinE1 or CyclinA" Prol~
4 fate "E2F1_2 or TP53" Apop~
5 fate "p21CIP or RB1 or RBL2" Grow~
6 gene "SPRY and not FGFR3 and not GRB2" EGFR
7 gene "not EGFR and not GRB2" FGFR3
8 gene "EGFR or FGFR3 or GRB2" RAS
9 gene "not RB1 and not RBL2 and ((not (CHEK1_2_2 and ATM_2) and (RAS o~ E2F1~
10 gene "not RBL2 and not RB1 and ATM_2 and CHEK1_2_2 and (RAS or E2F3_2~ E2F1~
11 gene "not RB1 and not CHEK1_2_2 and RAS" E2F3~
12 gene "not RB1 and CHEK1_2_2 and RAS" E2F3~
13 gene "(RAS or AKT) and not p16INK4a and not p21CIP" Cycl~
14 gene "not RBL2 and not p21CIP and CDC25A and ((E2F1_1 or E2F1_2) or (~ Cycl~
15 gene "not RBL2 and not p21CIP and CDC25A and ((E2F1_1 or E2F1_2) or (~ Cycl~
16 gene "not (CHEK1_2_1 or CHEK1_2_2) and not RBL2 and ((E2F1_1 or E2F1_~ CDC2~
17 gene "GrowthInhibitors and not RB1" p16I~
18 gene "not CyclinD1 and not CyclinE1 and not p16INK4a and not CyclinA" RB1
19 gene "not CyclinD1 and not CyclinE1" RBL2
20 gene "not CyclinE1 and (GrowthInhibitors or TP53) and not AKT" p21C~
21 gene "DNAdamage and not (E2F1_1 or E2F1_2)" ATM_1
22 gene "(E2F1_1 or E2F1_2) and DNAdamage" ATM_2
23 gene "(ATM_1 or ATM_2) and not (E2F1_1 or E2F1_2)" CHEK~
24 gene "(E2F1_1 or E2F1_2) and (ATM_1 or ATM_2)" CHEK~
25 gene "(TP53 or AKT) and not (E2F1_1 or E2F1_2) and not (ATM_1 or ATM_~ MDM2
26 gene "not MDM2 and (((ATM_1 or ATM_2) and (CHEK1_2_1 or CHEK1_2_2)) o~ TP53
27 gene "GRB2 and RAS and not TP53" PI3K
28 gene "PI3K" AKT
29 gene "(FGFR3 and not GRB2 and not SPRY) or EGFR" GRB2
30 gene "RAS" SPRY
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createNetworkGenesTemplate correctly returns the template file
Code
createNetworkGenesTemplate(network, store = F, modify = F)
Output
# A tibble: 25 x 2
node symbol
<chr> <chr>
1 EGFR EGFR
2 FGFR3 FGFR3
3 RAS RAS
4 E2F1_1 E2F1_1
5 E2F1_2 E2F1_2
6 E2F3_1 E2F3_1
7 E2F3_2 E2F3_2
8 CyclinD1 CyclinD1
9 CyclinE1 CyclinE1
10 CyclinA CyclinA
# ... with 15 more rows
ginmlToGraphml correctly returns a graphml file as a vector
Code
ginmlToGraphml(system.file("extdata", "example_ginsim.zginml", package = "ingres"),
dest = withr::local_tempfile(fileext = ".graphml"))
Output
[1] "<?xml version=\"1.0\" encoding=\"UTF-8\"?><graphml xmlns=\"http://graphml.graphdrawing.org/xmlns\">"
[2] "<key attr.name=\"kind\" attr.type=\"string\" for=\"node\" id=\"kind\"/>"
[3] "<key attr.name=\"rule\" attr.type=\"string\" for=\"node\" id=\"rule\"/>"
[4] "<key attr.name=\"sign\" attr.type=\"string\" for=\"edge\" id=\"sign\"/>"
[5] "<graph edgedefault=\"directed\">"
[6] "<node id=\"DNA_Damage\">"
[7] "<data key=\"kind\">input</data>"
[8] "</node>"
[9] "<node id=\"ATM\">"
[10] "<data key=\"rule\">DNA_Damage and (E2F1 or not Wip1 or not HDAC1)</data>"
[11] "<data key=\"kind\">gene</data>"
[12] "</node>"
[13] "<node id=\"p38MAPK\">"
[14] "<data key=\"rule\">ATM and not Wip1</data>"
[15] "<data key=\"kind\">gene</data>"
[16] "</node>"
[17] "<node id=\"Mdm2\">"
[18] "<data key=\"rule\">(not Wip1 or p53) and not ATM</data>"
[19] "<data key=\"kind\">gene</data>"
[20] "</node>"
[21] "<node id=\"p53\">"
[22] "<data key=\"rule\">ATM or (not Mdm2 and p38MAPK)</data>"
[23] "<data key=\"kind\">gene</data>"
[24] "</node>"
[25] "<node id=\"Wip1\">"
[26] "<data key=\"rule\">p53_A</data>"
[27] "<data key=\"kind\">gene</data>"
[28] "</node>"
[29] "<node id=\"p53_A\">"
[30] "<data key=\"rule\">not Sirt_1 and not p53_K and (p53:1 or not p53_INP1)</data>"
[31] "<data key=\"kind\">gene</data>"
[32] "</node>"
[33] "<node id=\"p53_K\">"
[34] "<data key=\"rule\">not p53_A and (not Sirt_1 or not Wip1) and p53</data>"
[35] "<data key=\"kind\">gene</data>"
[36] "</node>"
[37] "<node id=\"miR_34a\">"
[38] "<data key=\"rule\">ATM</data>"
[39] "<data key=\"kind\">gene</data>"
[40] "</node>"
[41] "<node id=\"p21\">"
[42] "<data key=\"rule\">p53_A or ((not HDAC1 or not c_Myc) and not Caspase3 and p38MAPK)</data>"
[43] "<data key=\"kind\">gene</data>"
[44] "</node>"
[45] "<node id=\"p53_INP1\">"
[46] "<data key=\"rule\">p53_K or p53_A</data>"
[47] "<data key=\"kind\">gene</data>"
[48] "</node>"
[49] "<node id=\"c_Myc\">"
[50] "<data key=\"rule\">(E2F1 or p38MAPK or not miR_34a) and not RB and not p21</data>"
[51] "<data key=\"kind\">gene</data>"
[52] "</node>"
[53] "<node id=\"Cdc25A\">"
[54] "<data key=\"rule\">(not ATM and not miR_34a) or not p38MAPK</data>"
[55] "<data key=\"kind\">gene</data>"
[56] "</node>"
[57] "<node id=\"cdk46_CycD\">"
[58] "<data key=\"rule\">Cdc25A and not miR_34a and not p21</data>"
[59] "<data key=\"kind\">gene</data>"
[60] "</node>"
[61] "<node id=\"cdk2_CycE\">"
[62] "<data key=\"rule\">Cdc25A and E2F1 and not miR_34a and not p21</data>"
[63] "<data key=\"kind\">gene</data>"
[64] "</node>"
[65] "<node id=\"RB\">"
[66] "<data key=\"rule\">not cdk46_CycD and not cdk2_CycE</data>"
[67] "<data key=\"kind\">gene</data>"
[68] "</node>"
[69] "<node id=\"E2F1\">"
[70] "<data key=\"rule\">(not RB and ((Cdc25A and ATM) or not Sirt_1 or not miR_34a)) or c_Myc</data>"
[71] "<data key=\"kind\">gene</data>"
[72] "</node>"
[73] "<node id=\"Sirt_1\">"
[74] "<data key=\"rule\">E2F1 and not (HDAC1 and miR_34a)</data>"
[75] "<data key=\"kind\">gene</data>"
[76] "</node>"
[77] "<node id=\"HDAC1\">"
[78] "<data key=\"rule\">(not miR_34a and not Sirt_1) or not DNA_Damage</data>"
[79] "<data key=\"kind\">gene</data>"
[80] "</node>"
[81] "<node id=\"PUMA\">"
[82] "<data key=\"rule\">p53_K</data>"
[83] "<data key=\"kind\">gene</data>"
[84] "</node>"
[85] "<node id=\"BCL2\">"
[86] "<data key=\"rule\">not PUMA and not miR_34a</data>"
[87] "<data key=\"kind\">gene</data>"
[88] "</node>"
[89] "<node id=\"BAX\">"
[90] "<data key=\"rule\">not BCL2 and p53_K</data>"
[91] "<data key=\"kind\">gene</data>"
[92] "</node>"
[93] "<node id=\"Caspase3\">"
[94] "<data key=\"rule\">not (BCL2 and p21) and BAX</data>"
[95] "<data key=\"kind\">gene</data>"
[96] "</node>"
[97] "<node id=\"Proliferation\">"
[98] "<data key=\"rule\">E2F1 and not p53</data>"
[99] "<data key=\"kind\">gene</data>"
[100] "</node>"
[101] "<node id=\"SIPS\">"
[102] "<data key=\"rule\">p21 and not E2F1</data>"
[103] "<data key=\"kind\">gene</data>"
[104] "</node>"
[105] "<node id=\"Apoptosis\">"
[106] "<data key=\"rule\">Caspase3</data>"
[107] "<data key=\"kind\">gene</data>"
[108] "</node>"
[109] "<edge source=\"Sirt_1\" target=\"p53_K\">"
[110] "<data key=\"sign\">negative</data>"
[111] "</edge>"
[112] "<edge source=\"Sirt_1\" target=\"p53_A\">"
[113] "<data key=\"sign\">negative</data>"
[114] "</edge>"
[115] "<edge source=\"Sirt_1\" target=\"E2F1\">"
[116] "<data key=\"sign\">negative</data>"
[117] "</edge>"
[118] "<edge source=\"Sirt_1\" target=\"HDAC1\">"
[119] "<data key=\"sign\">negative</data>"
[120] "</edge>"
[121] "<edge source=\"p53_INP1\" target=\"p53_A\">"
[122] "<data key=\"sign\">negative</data>"
[123] "</edge>"
[124] "<edge source=\"p53_A\" target=\"p53_K\">"
[125] "<data key=\"sign\">negative</data>"
[126] "</edge>"
[127] "<edge source=\"p53_A\" target=\"p21\">"
[128] "<data key=\"sign\">positive</data>"
[129] "</edge>"
[130] "<edge source=\"p53_A\" target=\"Wip1\">"
[131] "<data key=\"sign\">positive</data>"
[132] "</edge>"
[133] "<edge source=\"p53_A\" target=\"p53_INP1\">"
[134] "<data key=\"sign\">positive</data>"
[135] "</edge>"
[136] "<edge source=\"Mdm2\" target=\"p53\">"
[137] "<data key=\"sign\">negative</data>"
[138] "</edge>"
[139] "<edge source=\"Wip1\" target=\"ATM\">"
[140] "<data key=\"sign\">negative</data>"
[141] "</edge>"
[142] "<edge source=\"Wip1\" target=\"Mdm2\">"
[143] "<data key=\"sign\">negative</data>"
[144] "</edge>"
[145] "<edge source=\"Wip1\" target=\"p53_K\">"
[146] "<data key=\"sign\">negative</data>"
[147] "</edge>"
[148] "<edge source=\"Wip1\" target=\"p38MAPK\">"
[149] "<data key=\"sign\">negative</data>"
[150] "</edge>"
[151] "<edge source=\"p53_K\" target=\"p53_A\">"
[152] "<data key=\"sign\">negative</data>"
[153] "</edge>"
[154] "<edge source=\"p53_K\" target=\"p53_INP1\">"
[155] "<data key=\"sign\">positive</data>"
[156] "</edge>"
[157] "<edge source=\"p53_K\" target=\"BAX\">"
[158] "<data key=\"sign\">positive</data>"
[159] "</edge>"
[160] "<edge source=\"p53_K\" target=\"PUMA\">"
[161] "<data key=\"sign\">positive</data>"
[162] "</edge>"
[163] "<edge source=\"E2F1\" target=\"Sirt_1\">"
[164] "<data key=\"sign\">positive</data>"
[165] "</edge>"
[166] "<edge source=\"E2F1\" target=\"ATM\">"
[167] "<data key=\"sign\">positive</data>"
[168] "</edge>"
[169] "<edge source=\"E2F1\" target=\"c_Myc\">"
[170] "<data key=\"sign\">positive</data>"
[171] "</edge>"
[172] "<edge source=\"E2F1\" target=\"cdk2_CycE\">"
[173] "<data key=\"sign\">positive</data>"
[174] "</edge>"
[175] "<edge source=\"E2F1\" target=\"Proliferation\">"
[176] "<data key=\"sign\">positive</data>"
[177] "</edge>"
[178] "<edge source=\"E2F1\" target=\"SIPS\">"
[179] "<data key=\"sign\">negative</data>"
[180] "</edge>"
[181] "<edge source=\"cdk2_CycE\" target=\"RB\">"
[182] "<data key=\"sign\">negative</data>"
[183] "</edge>"
[184] "<edge source=\"ATM\" target=\"p53\">"
[185] "<data key=\"sign\">positive</data>"
[186] "</edge>"
[187] "<edge source=\"ATM\" target=\"Mdm2\">"
[188] "<data key=\"sign\">negative</data>"
[189] "</edge>"
[190] "<edge source=\"ATM\" target=\"E2F1\">"
[191] "<data key=\"sign\">positive</data>"
[192] "</edge>"
[193] "<edge source=\"ATM\" target=\"Cdc25A\">"
[194] "<data key=\"sign\">negative</data>"
[195] "</edge>"
[196] "<edge source=\"ATM\" target=\"p38MAPK\">"
[197] "<data key=\"sign\">positive</data>"
[198] "</edge>"
[199] "<edge source=\"ATM\" target=\"miR_34a\">"
[200] "<data key=\"sign\">positive</data>"
[201] "</edge>"
[202] "<edge source=\"p38MAPK\" target=\"p53\">"
[203] "<data key=\"sign\">positive</data>"
[204] "</edge>"
[205] "<edge source=\"p38MAPK\" target=\"c_Myc\">"
[206] "<data key=\"sign\">positive</data>"
[207] "</edge>"
[208] "<edge source=\"p38MAPK\" target=\"p21\">"
[209] "<data key=\"sign\">positive</data>"
[210] "</edge>"
[211] "<edge source=\"p38MAPK\" target=\"Cdc25A\">"
[212] "<data key=\"sign\">negative</data>"
[213] "</edge>"
[214] "<edge source=\"PUMA\" target=\"BCL2\">"
[215] "<data key=\"sign\">negative</data>"
[216] "</edge>"
[217] "<edge source=\"p21\" target=\"cdk46_CycD\">"
[218] "<data key=\"sign\">negative</data>"
[219] "</edge>"
[220] "<edge source=\"p21\" target=\"c_Myc\">"
[221] "<data key=\"sign\">negative</data>"
[222] "</edge>"
[223] "<edge source=\"p21\" target=\"Caspase3\">"
[224] "<data key=\"sign\">negative</data>"
[225] "</edge>"
[226] "<edge source=\"p21\" target=\"cdk2_CycE\">"
[227] "<data key=\"sign\">negative</data>"
[228] "</edge>"
[229] "<edge source=\"p21\" target=\"SIPS\">"
[230] "<data key=\"sign\">positive</data>"
[231] "</edge>"
[232] "<edge source=\"miR_34a\" target=\"HDAC1\">"
[233] "<data key=\"sign\">negative</data>"
[234] "</edge>"
[235] "<edge source=\"miR_34a\" target=\"E2F1\">"
[236] "<data key=\"sign\">negative</data>"
[237] "</edge>"
[238] "<edge source=\"miR_34a\" target=\"Sirt_1\">"
[239] "<data key=\"sign\">negative</data>"
[240] "</edge>"
[241] "<edge source=\"miR_34a\" target=\"BCL2\">"
[242] "<data key=\"sign\">negative</data>"
[243] "</edge>"
[244] "<edge source=\"miR_34a\" target=\"cdk46_CycD\">"
[245] "<data key=\"sign\">negative</data>"
[246] "</edge>"
[247] "<edge source=\"miR_34a\" target=\"cdk2_CycE\">"
[248] "<data key=\"sign\">negative</data>"
[249] "</edge>"
[250] "<edge source=\"miR_34a\" target=\"c_Myc\">"
[251] "<data key=\"sign\">negative</data>"
[252] "</edge>"
[253] "<edge source=\"miR_34a\" target=\"Cdc25A\">"
[254] "<data key=\"sign\">negative</data>"
[255] "</edge>"
[256] "<edge source=\"c_Myc\" target=\"p21\">"
[257] "<data key=\"sign\">negative</data>"
[258] "</edge>"
[259] "<edge source=\"c_Myc\" target=\"E2F1\">"
[260] "<data key=\"sign\">positive</data>"
[261] "</edge>"
[262] "<edge source=\"DNA_Damage\" target=\"ATM\">"
[263] "<data key=\"sign\">positive</data>"
[264] "</edge>"
[265] "<edge source=\"DNA_Damage\" target=\"HDAC1\">"
[266] "<data key=\"sign\">negative</data>"
[267] "</edge>"
[268] "<edge source=\"Caspase3\" target=\"p21\">"
[269] "<data key=\"sign\">negative</data>"
[270] "</edge>"
[271] "<edge source=\"Caspase3\" target=\"Apoptosis\">"
[272] "<data key=\"sign\">positive</data>"
[273] "</edge>"
[274] "<edge source=\"HDAC1\" target=\"p21\">"
[275] "<data key=\"sign\">negative</data>"
[276] "</edge>"
[277] "<edge source=\"HDAC1\" target=\"Sirt_1\">"
[278] "<data key=\"sign\">negative</data>"
[279] "</edge>"
[280] "<edge source=\"HDAC1\" target=\"ATM\">"
[281] "<data key=\"sign\">negative</data>"
[282] "</edge>"
[283] "<edge source=\"RB\" target=\"E2F1\">"
[284] "<data key=\"sign\">negative</data>"
[285] "</edge>"
[286] "<edge source=\"RB\" target=\"c_Myc\">"
[287] "<data key=\"sign\">negative</data>"
[288] "</edge>"
[289] "<edge source=\"p53\" target=\"p53_A\">"
[290] "<data key=\"sign\">positive</data>"
[291] "</edge>"
[292] "<edge source=\"p53\" target=\"Mdm2\">"
[293] "<data key=\"sign\">positive</data>"
[294] "</edge>"
[295] "<edge source=\"p53\" target=\"p53_K\">"
[296] "<data key=\"sign\">positive</data>"
[297] "</edge>"
[298] "<edge source=\"p53\" target=\"Proliferation\">"
[299] "<data key=\"sign\">negative</data>"
[300] "</edge>"
[301] "<edge source=\"Cdc25A\" target=\"E2F1\">"
[302] "<data key=\"sign\">positive</data>"
[303] "</edge>"
[304] "<edge source=\"Cdc25A\" target=\"cdk46_CycD\">"
[305] "<data key=\"sign\">positive</data>"
[306] "</edge>"
[307] "<edge source=\"Cdc25A\" target=\"cdk2_CycE\">"
[308] "<data key=\"sign\">positive</data>"
[309] "</edge>"
[310] "<edge source=\"cdk46_CycD\" target=\"RB\">"
[311] "<data key=\"sign\">negative</data>"
[312] "</edge>"
[313] "<edge source=\"BCL2\" target=\"BAX\">"
[314] "<data key=\"sign\">negative</data>"
[315] "</edge>"
[316] "<edge source=\"BCL2\" target=\"Caspase3\">"
[317] "<data key=\"sign\">negative</data>"
[318] "</edge>"
[319] "<edge source=\"BAX\" target=\"Caspase3\">"
[320] "<data key=\"sign\">positive</data>"
[321] "</edge>"
[322] "</graph>"
[323] "</graphml>"
printAllNodes correctly prints a network
Code
printAllNodes(network)
Output
# A tibble: 30 x 3
kind rule id
<chr> <chr> <chr>
1 input "" DNAd~
2 input "" Grow~
3 fate "CyclinE1 or CyclinA" Prol~
4 fate "E2F1_2 or TP53" Apop~
5 fate "p21CIP or RB1 or RBL2" Grow~
6 gene "SPRY and not FGFR3 and not GRB2" EGFR
7 gene "not EGFR and not GRB2" FGFR3
8 gene "EGFR or FGFR3 or GRB2" RAS
9 gene "not RB1 and not RBL2 and ((not (CHEK1_2_2 and ATM_2) and (RAS o~ E2F1~
10 gene "not RBL2 and not RB1 and ATM_2 and CHEK1_2_2 and (RAS or E2F3_2~ E2F1~
11 gene "not RB1 and not CHEK1_2_2 and RAS" E2F3~
12 gene "not RB1 and CHEK1_2_2 and RAS" E2F3~
13 gene "(RAS or AKT) and not p16INK4a and not p21CIP" Cycl~
14 gene "not RBL2 and not p21CIP and CDC25A and ((E2F1_1 or E2F1_2) or (~ Cycl~
15 gene "not RBL2 and not p21CIP and CDC25A and ((E2F1_1 or E2F1_2) or (~ Cycl~
16 gene "not (CHEK1_2_1 or CHEK1_2_2) and not RBL2 and ((E2F1_1 or E2F1_~ CDC2~
17 gene "GrowthInhibitors and not RB1" p16I~
18 gene "not CyclinD1 and not CyclinE1 and not p16INK4a and not CyclinA" RB1
19 gene "not CyclinD1 and not CyclinE1" RBL2
20 gene "not CyclinE1 and (GrowthInhibitors or TP53) and not AKT" p21C~
21 gene "DNAdamage and not (E2F1_1 or E2F1_2)" ATM_1
22 gene "(E2F1_1 or E2F1_2) and DNAdamage" ATM_2
23 gene "(ATM_1 or ATM_2) and not (E2F1_1 or E2F1_2)" CHEK~
24 gene "(E2F1_1 or E2F1_2) and (ATM_1 or ATM_2)" CHEK~
25 gene "(TP53 or AKT) and not (E2F1_1 or E2F1_2) and not (ATM_1 or ATM_~ MDM2
26 gene "not MDM2 and (((ATM_1 or ATM_2) and (CHEK1_2_1 or CHEK1_2_2)) o~ TP53
27 gene "GRB2 and RAS and not TP53" PI3K
28 gene "PI3K" AKT
29 gene "(FGFR3 and not GRB2 and not SPRY) or EGFR" GRB2
30 gene "RAS" SPRY
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