tests/testthat/test-plot_volcano.R

testthat::context("Testing plot_volcano function")

testthat::test_that("Test if plot_volcano runs", {
  set.seed(42)

  # de_res<-de_res_test;pvalue <-0.2;lfc_threshold<-1.4;fdr<-TRUE;
  de_res_test <- structure(
    list(
      gene = c("AAEL000001", "AAEL000004", "AAEL000005", "AAEL000006", "AAEL000008", "AAEL000010", "AAEL000011", "AAEL000012", "AAEL000013", "AAEL000016", "AAEL000017", "AAEL000018", "AAEL000020", "AAEL000021", "AAEL000022", "AAEL000024", "AAEL000025", "AAEL000026", "AAEL000027", "AAEL000028", "AAEL000029", "AAEL000032", "AAEL000033", "AAEL000035", "AAEL000036", "AAEL000037", "AAEL000038", "AAEL000039", "AAEL000041", "AAEL000042", "AAEL000043", "AAEL000044", "AAEL000046", "AAEL000047", "AAEL000048", "AAEL000049", "AAEL000050", "AAEL000051", "AAEL000053", "AAEL000055", "AAEL000057", "AAEL000058", "AAEL000063", "AAEL000064", "AAEL000065", "AAEL000066", "AAEL000069", "AAEL000071", "AAEL000073", "AAEL000074", "AAEL000075", "AAEL000076", "AAEL000077", "AAEL000079", "AAEL000080", "AAEL000081", "AAEL000084", "AAEL000085", "AAEL000087", "AAEL000088", "AAEL000089", "AAEL000090", "AAEL000091", "AAEL000092", "AAEL000094", "AAEL000095", "AAEL000097", "AAEL000098", "AAEL000099", "AAEL000101", "AAEL000102", "AAEL000106", "AAEL000107", "AAEL000108", "AAEL000109", "AAEL000111", "AAEL000113", "AAEL000115", "AAEL000116", "AAEL000117", "AAEL000118", "AAEL000119", "AAEL000122", "AAEL000123", "AAEL000124", "AAEL000126", "AAEL000127", "AAEL000128", "AAEL000134", "AAEL000137", "AAEL000138", "AAEL000139", "AAEL000140", "AAEL000143", "AAEL000146", "AAEL000147", "AAEL000148", "AAEL000149", "AAEL000151", "AAEL000152"),
      baseMean = c(1347.67893559122, 2085.92917291839, 1834.69280842695, 6097.88942694284, 1696.61251345575, 6431.40495962188, 0.991033180443822, 29.7183081511896, 556.026127957344, 661.448773096139, 0.961654539974706, 0.56893341547563, 1647.64909234668, 9.58429111034313, 454.351736102443, 373.986798974077, 4.37876538582306, 439.508720459672, 0.562635719553954, 2637.5381895404, 1.77592690594228, 26683.4802136034, 1011.82102586577, 100.755322055838, 0.183621076598902, 617.511367570421, 721.969118160311, 1.74776099689257, 56.0970076657724, 665.444662802439, 3.45800015272126, 1788.44384517712, 1046.50750682923, 0.271306129948915, 9.37278830558761, 264.363997804894, 586.512172964621, 53.8038023630155, 1611.28454347627, 1489.85425676306, 46.1164143168121, 44.9954801110326, 1.67830045010877, 2649.91686164475, 936.532999060728, 24.2221334561634, 1.69323039091362, 10.2810604224596, 44.8103864211679, 1016.51273431512, 2.18358862481209, 563.983108437243, 1460.54670235214, 6112.76855615765, 2543.33398741054, 8127.93132134589, 2593.08299472595, 17.4126733920008, 1148.70506294011, 1326.7272803733, 1.93078935529758, 3159.9414926424, 1830.02665226232, 178.432109233637, 17.3429639956481, 2.16387161968027, 7.53830256881158, 6.03508349885534, 403.103963450852, 211.767480323212, 2173.32021819667, 455.308592911171, 506.93212170761, 4.0600783463442, 5620.87320417886, 1860.63459878636, 1.11383638445279, 993.908787122769, 881.587249835213, 0.568322670576471, 1397.35675191662, 184.085635364835, 1956.425777703, 7.21821468736391, 447.409432627576, 741.520328704975, 76.3163539927285, 4484.00137330472, 120.575411445996, 153.366265836596, 1431.15729003393, 38.3516161395473, 685.524516229694, 746.302243196322, 39.8422332915052, 494.945045389236, 369.006127715014, 2067.77660386387, 1.96268226017258, 92.9579685686906),
      log2FoldChange = rnorm(100, 0, 1),
      lfcSE = c(0.0820596487642601, 0.105047117012213, 0.100545402485417, 0.126350404538118, 0.119881091112529, 0.139601815020943, 0.0301328804742501, 0.0787627943256495, 0.109602957282432, 0.107765719629104, 0.0231937496199589, 0.0226857917261912, 0.102317192956139, 0.0609298165214452, 0.107753648181465, 0.135579911537413, 0.0653659305196352, 0.12439115363428, 0.0227403927562215, 0.125313678835833, 0.0433224931500374, 0.117573090263384, 0.119571004351523, 0.134088718474395, 0.0223377132275914, 0.130497908776535, 0.104427063644348, 0.037571300637267, 0.099666035489178, 0.0978154690856593, 0.065446262446961, 0.136974231809931, 0.0883104466838645, 0.0223862739489468, 0.0830246230140929, 0.140349261943718, 0.109351619390515, 0.129296692961314, 0.115260961702648, 0.0956544804609969, 0.110579441142384, 0.0650261338757476, 0.0443343785989794, 0.0855681170133386, 0.109494932324506, 0.111965021457106, 0.0380618213854908, 0.0856581835451659, 0.126960962890127, 0.140923563300902, 0.0414523879697469, 0.119571596969158, 0.0924618736694562, 0.0996370919026078, 0.122312558279876, 0.100123621544037, 0.0893956228381483, 0.0889444034335185, 0.114219677224032, 0.0982612292788794, 0.0488823723986813, 0.0693864725691609, 0.127718069827566, 0.133860710102815, 0.0934697177116821, 0.0496425276922542, 0.0863409788808191, 0.070521130977437, 0.140114961580841, 0.140877364535706, 0.138722804180839, 0.131790051988343, 0.120725715278105, 0.0654218674632276, 0.117764677990964, 0.0818012141611601, 0.0369090671554646, 0.112138374073205, 0.102286882308735, 0.0225559514540793, 0.0889006694606414, 0.134851563772467, 0.0983913529323541, 0.0762313526106918, 0.139583589442353, 0.134661177145752, 0.135707334358806, 0.0721296606561992, 0.140158999755765, 0.138760811265089, 0.0907777302615168, 0.126659545812527, 0.105120878321883, 0.0968682738755512, 0.119109888510878, 0.110056595312303, 0.121627725232952, 0.114809633237201, 0.0375466794226115, 0.129489290731185),
      stat = c(0.143370826837919, 1.10860419146462, 0.580791697735623, -0.581139489731591, 0.560686975279181, -0.580729465117072, -0.868022111251453, -0.919050573259781, 0.89168211421288, -0.616569064553351, -0.421437738955418, -0.407428289580928, 0.151368208184423, -0.0066182053659054, 0.0202173749169503, -0.571320954258, -0.225752584046186, -0.758811106877811, -0.233833884426901, -1.01625002976123, -0.321396148166654, 0.65468164562887, 0.707340425833148, 0.49157649926022, -0.0101890019348365, -0.726760664881976, -0.538028664092355, 0.00493095206642874, -1.50647996016193, 1.17648766825581, 0.187936265030725, -1.50986696543311, 1.09894516706887, -0.162967404211592, -0.302459386565981, -0.877948497706889, -0.8720055502761, -1.01199848498817, -0.342268534043752, -0.630468583966625, 0.288994752886624, -2.35255537506811, -0.591346233828736, 0.625622652739121, -0.121866504913492, -0.705673654931742, 0.198829172906168, 0.0774418711701307, 0.195616390431531, -0.970488496182446, -0.202793237277068, -0.242729937299476, 0.422007311193995, 1.06741186270853, 0.104469676613195, 1.06764223802556, -0.0771529027056695, -1.25786213110372, 0.75592802119935, 0.301505456269054, 0.228191138864655, -1.24495950799115, 0.0072114754093155, -0.549933600847927, -0.516568962015238, -0.710443373097414, 0.253381482890435, 0.835158677348995, 0.0901650798778941, 0.538801580736019, -1.0617369242117, -0.939258829579683, 1.31460729197136, 0.739378174803055, -1.26513069924339, 0.325373581684489, 0.0894512457509433, 0.97340577831218, 0.153660559680593, -0.385443596273284, 1.66210367111819, -0.32905456843546, 0.322407511749947, -0.616712542854078, -1.16453484170352, -0.355637689961633, 0.740140911745842, -0.0270759818059361, -0.837619660596344, 0.155911616466053, 1.22927502693789, -0.942906963632297, 0.204702576566544, 0.717890830714137, -0.458657574130205, -0.0402207350331602, 0.260261452438783, -0.315161567209738, -0.256122004928037, -0.355523304307489),
      pvalue = c(0.00000097321737519, 0.267600969161314, 0.561380851214951, 0.56114644566802, 0.575010947804443, 0.561422799875263, 0.3853822281877, 0.358069120304049, 0.372563342952272, 0.537519004498738, 0.673435466361034, 0.683693452829374, 0.879685266659827, 0.99471947466675, 0.98386996753891, 0.567782100151945, 0.821393857464912, 0.447965560558812, 0.815113942734387, 0.309510337738967, 0.747910201735104, 0.512672744947411, 0.479354949004661, 0.623018760185287, 0.991870493328266, 0.467372583321403, 0.590557259633323, 0.996065685419487, 0.131944007755575, 0.239400057384934, 0.850926613844855, 0.131077373472667, 0.271791983849465, 0.870544099201241, 0.762301889259154, 0.37997166867314, 0.383205349673378, 0.311538777804425, 0.732148813318378, 0.528388050954354, 0.772585392915951, 0.0186449133977225, 0.554288457424595, 0.531562476978378, 0.903004743067582, 0.480391108052339, 0.842396374893907, 0.93827203239893, 0.844910430421824, 0.331803056302674, 0.839296643984886, 0.808214614265804, 0.673019680939892, 0.285785894003849, 0.916796631135276, 0.28568192306373, 0.938501908107086, 0.208441621109638, 0.449692352483341, 0.763029089974263, 0.81949764989485, 0.213146634818471, 0.994246124982415, 0.582364916770626, 0.605457087042307, 0.477429234682302, 0.799973435392681, 0.403628372539264, 0.928156033484586, 0.590023772786687, 0.288355131683986, 0.347597870982362, 0.188641918161594, 0.459677391330586, 0.205824479682198, 0.744898347427189, 0.928723298443016, 0.330351668194781, 0.877877384179974, 0.699908787804658, 0.096491989638425, 0.742114442832143, 0.747143994253445, 0.537424346582062, 0.244207332086512, 0.722111914074244, 0.459214496560281, 0.978399131478473, 0.402244347270675, 0.876102688672504, 0.218968707174679, 0.345728492724397, 0.837804507228365, 0.472824601984319, 0.646480085003645, 0.967917146838195, 0.794662104738394, 0.752638984590235, 0.797856631070674, 0.722197589460159),
      padj = c(0.999823509997326, 0.999823509997326, 0.999823509997326, 0.999823509997326, 0.999823509997326, 0.999823509997326, NA, 0.999823509997326, 0.999823509997326, 0.999823509997326, NA, NA, 0.999823509997326, NA, 0.999823509997326, 0.999823509997326, NA, 0.999823509997326, NA, 0.999823509997326, NA, 0.999823509997326, 0.999823509997326, 0.999823509997326, NA, 0.999823509997326, 0.999823509997326, NA, 0.999823509997326, 0.999823509997326, NA, 0.999823509997326, 0.999823509997326, NA, NA, 0.999823509997326, 0.999823509997326, 0.999823509997326, 0.999823509997326, 0.999823509997326, 0.999823509997326, 0.956023595879174, NA, 0.999823509997326, 0.999823509997326, 0.999823509997326, NA, NA, 0.999823509997326, 0.999823509997326, NA, 0.999823509997326, 0.999823509997326, 0.999823509997326, 0.999823509997326, 0.999823509997326, 0.999823509997326, 0.999823509997326, 0.999823509997326, 0.999823509997326, NA, 0.999823509997326, 0.999823509997326, 0.999823509997326, 0.999823509997326, NA, NA, NA, 0.999823509997326, 0.999823509997326, 0.999823509997326, 0.999823509997326, 0.999823509997326, NA, 0.999823509997326, 0.999823509997326, NA, 0.999823509997326, 0.999823509997326, NA, 0.999823509997326, 0.999823509997326, 0.999823509997326, NA, 0.999823509997326, 0.999823509997326, 0.999823509997326, 0.999823509997326, 0.999823509997326, 0.999823509997326, 0.999823509997326, 0.999823509997326, 0.999823509997326, 0.999823509997326, 0.999823509997326, 0.999823509997326, 0.999823509997326, 0.999823509997326, NA, 0.999823509997326)
    ),
    row.names = c(NA, -100L),
    class = c("tbl_df", "tbl", "data.frame")
  )



  res1 <- plot_volcano(de_res_test)

  testthat::expect_equal(tail(res1$data$gene), c(
    "AAEL000146", "AAEL000147", "AAEL000148", "AAEL000149", "AAEL000151",
    "AAEL000152"
  ))

  plot_volcano(de_res_test, fdr = TRUE, lfc_threshold = 0)

  plot_volcano(de_res_test, fdr = TRUE, pvalue = 0.2)

  plot_volcano(de_res_test, fdr = T, pvalue = .2, lfc_threshold = 0.2)

  plot_volcano(de_res_test, pvalue = 0.05)

  res2 <- plot_volcano(de_res_test, fdr = F, pvalue = .05, lfc_threshold = 0.2)


  testthat::expect_equal(res2$labels$label[1], "gene")


  res3 <- plot_volcano(de_res_test, pvalue = 0.05, lfc_threshold = 20)

  testthat::expect_equal(class(res3), c("gg", "ggplot"))
})

# de_res <- de_res_test
luciorq/txomics documentation built on Sept. 3, 2020, 5:36 a.m.