Open coynie opened 5 years ago
Hi @coynie , could you provide a minimally reproducible example? This would help me in trying to debug the issue.
Thanks!
Sure try this. I'm using couplet's plot grid() to put all the plots together but the issue also appears when calling the single plot. Thanks!
`#load required packages library(tidyverse) library(dabestr) library(cowplot)
wlSNs_nobeta <- structure(list(id = c(8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28), abs_raA = c(117.142857142857, 98.5714285714286, 112.857142857143, 215.714285714286, 377.142857142857, 185.714285714286, 77.1428571428571, 84.2857142857143, 60, 128.571428571429, 168.333333333333, 175, 72.1428571428571, 145.714285714286, 105.714285714286, 288.571428571429, 51.4285714285714, 364.285714285714), abs_raC = c(308.095238095238, 197.142857142857, 170, 424.761904761905, 368.571428571429, 291.904761904762, 312.857142857143, 101.904761904762, 159.52380952381, 212.380952380952, 376, 316.5, 155, 241.428571428571, 198.095238095238, 358.333333333333, 108.571428571429, 420), abs_raCA = c(190.952380952381, 98.5714285714286, 57.1428571428571, 209.047619047619, -8.57142857142861, 106.190476190476, 235.714285714286, 17.6190476190476, 99.5238095238095, 83.8095238095238, 207.666666666667, 141.5, 82.8571428571429, 95.7142857142857, 92.3809523809524, 69.7619047619048, 57.1428571428571, 55.7142857142857 ), abs_raACWR = c(0.380216383307573, 0.5, 0.663865546218487, 0.507847533632287, 1.02325581395349, 0.636215334420881, 0.246575342465753, 0.827102803738318, 0.376119402985075, 0.605381165919283, 0.447695035460993, 0.552922590837283, 0.465437788018433, 0.603550295857988, 0.533653846153846, 0.80531561461794, 0.473684210526316, 0.86734693877551), change_raA = c(-288.571428571429, -201.428571428571, -270, -567.142857142857, -60, -118.571428571429, -298.571428571429, 21.4285714285714, -212.857142857143, -180, -298.095238095238, -199.285714285714, -193.571428571429, -91.4285714285714, -271.428571428571, -118.571428571429, -214.285714285714, 80), change_raC = c(-95.2380952380952, -51.9047619047619, -112.857142857143, -104.52380952381, 25.7142857142857, -15.2380952380952, -160.952380952381, -78.5714285714286, -187.619047619048, -125, -83.7619047619048, -52.0714285714286, -83.5714285714286, -38.0952380952381, -271.904761904762, -45.952380952381, -127.142857142857, 18.0952380952381 ), change_raCA = c(193.333333333333, 149.52380952381, 157.142857142857, 462.619047619048, 85.7142857142857, 103.333333333333, 137.619047619048, -100, 25.2380952380952, 54.9999999999999, 214.333333333333, 147.214285714286, 110, 53.3333333333333, -0.476190476190439, 72.6190476190476, 87.1428571428571, -61.9047619047619), change_raACWR = c(-0.625686804413796, -0.704588910133843, -0.689669807316866, -0.971234787555297, -0.251744186046512, -0.354482339997724, -0.54638948165485, 0.478817843316154, -0.4098888274676, -0.309227161533081, -0.566805223472202, -0.462581285131709, -0.648334667071387, -0.244831305504874, -0.268777764788403, -0.201751523191247, -0.653588516746411, 0.160000967211529), vol_raA = c(134.400009255403, 54.690755317523, 81.8029940453958, 228.796084324313, 52.1116764473897, 52.17048005635, 114.791863873978, 29.1042160792213, 75.3007252458179, 69.6089312098585, 158.892986495762, 55.996537793849, 60.2162849386883, 56.2372974535452, 89.7174053792704, 41.6757521678502, 54.3074607355673, 83.5213234296735), vol_raC = c(39.2969612156178, 22.5100008967927, 30.3345454109121, 59.7468903635099, 20.3757225154646, 9.31105907969749, 59.6666675715245, 39.2989807875536, 57.4372542068637, 46.8911717595761, 54.6856681207061, 17.7416134330766, 24.929790192568, 12.4435015145565, 89.8737972253737, 28.4832255319214, 34.8864602927696, 24.6249044555942 ), vol_raCA = c(97.6690486403154, 38.4977179847517, 63.2065120705485, 204.750336513382, 53.7078987373672, 46.3583456339043, 69.9798974636487, 65.5017101370811, 26.8764575294767, 29.8834253794117, 106.722245198119, 39.8097886075452, 37.8517445059315, 51.7648471002637, 19.8142764227355, 26.9382580002514, 27.9062013512788, 76.8923734958472), vol_raACWR = c(0.28429919291267, 0.171475792832436, 0.244322639207408, 0.373651133819046, 0.145425433431645, 0.155955657305554, 0.215185142559467, 0.431139025365937, 0.176125761252924, 0.126149217953567, 0.259407332307541, 0.122717923733346, 0.201250420355636, 0.19919646372914, 0.092689253646399, 0.0672587677321364, 0.168539028726557, 0.192878218038433), abs_ewma1A = c(119.000513795851, 106.643368888931, 111.387428539078, 221.144496813386, 331.567343001678, 160.587893859214, 99.4100466130151, 72.836148777051, 81.6535945857512, 120.177325421192, 124.863369007239, 155.523648087284, 68.8930722842997, 140.583503512754, 80.3738608682444, 201.884482756256, 52.9528674472491, 344.826336948895), abs_ewma1C = c(236.254644679062, 171.464595099452, 160.966248540278, 346.807174449879, 364.692626725041, 240.57877338261, 249.739004607213, 106.537786969847, 143.340274138407, 187.80021906227, 263.03773343222, 269.347489800666, 131.593427322217, 203.508843222624, 181.082468613815, 318.431863584711, 108.695947361405, 399.1155344357 ), abs_ewma1CA = c(117.254130883211, 64.8212262105204, 49.5788200011999, 125.662677636493, 33.1252837233632, 79.990879523396, 150.328957994198, 33.7016381927958, 61.6866795526559, 67.6228936410777, 138.17436442498, 113.823841713382, 62.7003550379175, 62.9253397098706, 100.70860774557, 116.547380828455, 55.7430799141559, 54.2891974868048), abs_ewma1ACWR = c(0.503695975829411, 0.621955621958438, 0.691992449033227, 0.6376583678356, 0.90916930780633, 0.667506495279279, 0.398055749318639, 0.683664930994537, 0.569648656503251, 0.639921114156658, 0.474697555282176, 0.577408938180124, 0.523529736144111, 0.690798008020543, 0.443852248555621, 0.633995858591424, 0.487165057508402, 0.863976235443797), change_ewma1A = c(-247.479397574522, -125.167514727307, -335.116905625623, -619.607631419535, -193.409486690768, -162.476517568277, -335.985522275293, -16.3380132047176, -142.139422314612, -160.110506645666, -380.843476101779, -155.693177478515, -223.513427328224, -136.188957934618, -296.295982747113, -281.400361905739, -174.986071577384, 86.615804004321), change_ewma1C = c(-116.573017168172, -46.9713592153722, -143.105905458055, -241.996771980647, -13.8303401133433, -50.2130049197111, -199.516425167813, -37.2557511659476, -115.119654316466, -114.763856232343, -173.889154977408, -68.1105112142749, -112.847740234337, -28.4048913522242, -227.175750781799, -82.0837454936471, -113.96748014844, 93.3714663554437), change_ewma1CA = c(130.906380406349, 78.1961555119344, 192.011000167567, 377.610859438888, 179.579146577424, 112.263512648566, 136.469097107481, -20.9177379612299, 27.0197679981468, 45.346650413323, 206.954321124371, 87.58266626424, 110.665687093886, 107.784066582394, 69.1202319653141, 199.316616412092, 61.0185914289439, 6.75566235112274), change_ewma1ACWR = c(-0.534997842709821, -0.439274816699738, -0.776423281554021, -0.790239888162458, -0.477739481579207, -0.443475435893539, -0.571093514177948, 0.0635107631656937, -0.296222576373137, -0.286454007522729, -0.682719986471191, -0.344829754130568, -0.67269470728918, -0.502630496568715, -0.478774230766657, -0.572660845186241, -0.536527704135424, 0.0194446160215185), vol_ewma1A = c(133.058943289248, 58.154376791002, 80.0022899860389, 212.773616734812, 62.2977569777029, 62.5272202473118, 125.880561244335, 24.293102991733, 74.2126805049861, 72.4987165719818, 161.916803259578, 69.3971879944651, 61.2987495871907, 62.9597383731531, 93.9933335554993, 78.6035209207713, 50.4804137523572, 95.8782703975514), vol_ewma1C = c(60.4288474357636, 24.388559079803, 37.4089616754015, 94.3846758176754, 25.5653635138887, 23.6340854545295, 64.9306148275604, 9.80860196770636, 45.7234291416375, 43.8366127829923, 76.2975300783642, 28.0936907267791, 33.2550918223923, 26.2677802163546, 71.5813431589987, 28.1715656161128, 33.8729621637774, 51.0993014129225 ), vol_ewma1CA = c(77.1454818672372, 35.8493241401187, 45.9609658264543, 129.249914970496, 43.0094060720612, 41.2228517805564, 62.5939951062421, 21.9830139196358, 30.3658353689791, 31.5750544615464, 91.4483272128544, 42.0565280424247, 29.4425296918994, 43.1850605707931, 26.876612659395, 53.3687516047934, 18.4316074100456, 56.6895426827224), vol_ewma1ACWR = c(0.242492105948462, 0.170430303448065, 0.187631910235743, 0.250022163148667, 0.113554041340076, 0.146197862587291, 0.211796915409643, 0.169442352520555, 0.179875896539722, 0.132612179620373, 0.24082518417007, 0.136728182832202, 0.172003262084573, 0.178104515964331, 0.142171539758038, 0.142711407051194, 0.144138813733478, 0.135696948703938), abs_ewma2A = c(183.918560064379, 145.316223039074, 138.263888252649, 287.874401929521, 362.341652014512, 210.088238871599, 181.839209611985, 94.5225575268521, 110.914679311641, 155.20582192806, 200.452696056051, 226.561702973587, 103.090922444334, 179.808512534344, 130.399314875075, 278.376752962211, 82.1927558295064, 389.891222685059 ), abs_ewma2C = c(264.478261800536, 175.463960750135, 168.408379962856, 367.934442127866, 326.151827721931, 249.26898853511, 304.60138980156, 110.044141167933, 168.513637455178, 212.444710060945, 299.740057372783, 288.52740139959, 151.622763873964, 201.237797909154, 233.867232870284, 316.960043351866, 131.829932971608, 363.184762572632), abs_ewma2CA = c(80.5597017361575, 30.147737711061, 30.1444917102073, 80.0600401983447, -36.1898242925814, 39.1807496635109, 122.762180189576, 15.5215836410814, 57.5989581435376, 57.2388881328847, 99.2873613167322, 61.9656984260027, 48.5318414296308, 21.4292853748094, 103.467917995209, 38.5832903896554, 49.6371771421013, -26.7064601124274), abs_ewma2ACWR = c(0.695401424723088, 0.828182735747131, 0.821003612071704, 0.782406779492196, 1.1109600536209, 0.842817392192401, 0.596974326776539, 0.85895129466825, 0.658194084387634, 0.730570424104867, 0.668755113390635, 0.785234615064568, 0.679917182686548, 0.893512622392721, 0.557578388706559, 0.878270806687066, 0.623475670333598, 1.07353408750756), change_ewma2A = c(-188.000572544508, -94.6226948922742, -229.298043683799, -418.99468462549, -83.7365303248213, -95.7725933788113, -270.166750080467, -40.0820691450345, -147.823679067487, -149.727917432235, -275.96458738209, -112.025151782666, -163.736804971735, -77.4121643981451, -276.491105899767, -171.036917612525, -150.80131952528, 87.6574442040162), change_ewma2C = c(-15.1298155305186, 13.9508762820792, -43.0710704494082, -43.56604601394, 55.4030645311743, 7.69796429391823, -81.4087723040039, -9.40538004332096, -41.7831354990953, -42.02682856784, -37.6566517221904, -2.41391140889039, -41.5799021424581, 26.8625634063856, -115.852250689044, 20.3759672019833, -50.9787633626888, 110.157539240527), change_ewma2CA = c(172.870757013989, 108.573571174353, 186.226973234391, 375.42863861155, 139.139594855996, 103.47055767273, 188.757977776463, 30.6766891017135, 106.040543568392, 107.701088864395, 238.3079356599, 109.611240373775, 122.156902829277, 104.274727804531, 160.638855210723, 191.412884814509, 99.8225561625915, 22.5000950365105 ), change_ewma2ACWR = c(-0.634743026606677, -0.657386800130337, -0.917046733812549, -0.935377541364842, -0.536612319683156, -0.423314724484928, -0.57399474105033, -0.26792326545518, -0.572154602110695, -0.467731519615144, -0.743283802804114, -0.378528796490313, -0.701159657078116, -0.581586050110605, -0.605898168657781, -0.637028586351214, -0.651048354107328, -0.120937299803811), vol_ewma2A = c(91.9588815840292, 40.3889973556659, 58.7031932372458, 151.729907666619, 35.5185765807231, 38.1794122199367, 90.7060688363441, 13.2144033744877, 61.2996027191368, 58.7724764068333, 115.597176887869, 43.6703483719149, 47.000566130851, 39.6063463849827, 86.5775660333691, 46.7945288566893, 43.9439765525937, 64.9267667721921 ), vol_ewma2C = c(27.3896345921318, 12.190312739752, 10.8210057549351, 33.2054696138874, 28.214398546402, 13.6255152657358, 30.2000394227757, 4.2493925930861, 19.9843949810855, 18.7532851476218, 30.9551909492202, 15.5759988448038, 13.4632676578819, 20.3572012564723, 37.3367368630928, 23.1119297729738, 15.6842926104954, 44.1529912478655), vol_ewma2CA = c(72.797721992427, 39.0432587430069, 48.9816314175276, 129.128658513725, 31.4404883631809, 34.0948100828694, 62.1521421762724, 9.15903819874985, 42.7990028743541, 41.2571869728855, 91.8596997717577, 35.6112233031997, 34.9199698346061, 35.5389201374803, 50.2181685846357, 47.793724733221, 28.8803401893618, 32.7914500440276), vol_ewma2ACWR = c(0.236116019346408, 0.214246094117512, 0.243540782254956, 0.299051175368149, 0.123183014043921, 0.130683044094494, 0.179752325510558, 0.0787023792160263, 0.214621895529561, 0.165285357463659, 0.255045062275643, 0.11530832512659, 0.194289221069225, 0.176818437082674, 0.179778338641324, 0.154943630723732, 0.181602058178967, 0.0864283357820412), abs_strain = c(0.511624724594905, 0.994996841658075, 1.25990774607263, 1.69506063680318, 1.29697240783637, 1.39741867551076, 0.764184950247154, 0.850175866113747, 1.40129809949074, 1.32510649335428, 1.59225995946228, 0.862267768891004, 1.01531042371759, 1.10059838295304, 0.98886659507597, 0.775364737520656, 0.952661023244934, 1.30078340653854), abs_mono = c(419.532274167822, 686.547820744072, 995.327119397379, 2559.54156157281, 3424.00715668802, 1816.64427816399, 412.659873133463, 501.60376100711, 588.545201786111, 1192.59584401885, 1608.1825590569, 905.381157335554, 512.731763977381, 1122.6103506121, 731.761280356218, 1566.23676979173, 342.957968368176, 3316.99768667326), change_strain = c(-1.10999736698528, -0.39621984562243, -0.0104817580762235, -0.18843453838751, -0.37869001293898, 0.0437478983708457, -0.869428950673985, -0.444501883826553, -0.0729132754098638, 0.358051099170145, 0.414966526317288, -1.15198489235101, -0.424417536845587, -0.909100593161162, -0.202035447545743, -0.769121974221751, -0.360752885519826, -0.334323770175296), change_mono = c(-4185.8744659199, -2235.00722254499, -2409.31675172155, -7762.0119984722, -1703.51985088455, -1066.67447714403, -3883.74468628913, -68.0544489666212, -2227.19852427404, -896.243807418881, -2235.68050016149, -4371.96081511852, -2165.16224267012, -2213.48994973748, -2412.2201121651, -2835.55035867414, -2099.99190193428, 63.1344050127409 ), mean_strain = c(1.13412228876208, 1.49497808625493, 1.15429109715176, 1.60326658292368, 1.54470490693682, 1.61892543027148, 1.38253058775848, 1.35411560994399, 1.39945225046909, 1.26553641440904, 1.24798656167442, 1.75790781276539, 1.5025664464122, 1.6108887263159, 1.21263893160127, 1.35062809319368, 1.34258148984896, 1.41025386531569), mean_mono = c(3048.22250604434, 2459.2726656218, 1719.06076210491, 5772.58813124984, 4240.70963346739, 3518.79534807063, 3639.60137244606, 972.012259299196, 1890.705860162, 2050.14883234255, 3395.44461984326, 4409.41285323894, 1916.59787912395, 2983.34692677836, 2088.77161757183, 3903.0625690138, 1332.57561844879, 4098.10619089067), group1 = c("ns", "ns", "ns", "ns", "ns", "ns", "ns", "ns", "s", "s", "s", "s", "s", "s", "s", "s", "s", "s"), group2 = c("bot5", "bot5", "bot5", "bot5", "bot5", "na", "na", "na", "na", "na", "na", "na", "na", "top5", "top5", "top5", "top5", "top5"), pb = c(0.933099, 0.945946, 0.95122, 0.961538, 0.965368, 0.96962, 0.976798, 0.983333, 0.997167, 1, 1, 1.006289, 1.006711, 1.0131, 1.018041, 1.029412, 1.02973, 1.051793), wr = c(0.960144927536232, 0.921052631578947, 0.898617511520737, 0.921658986175115, 0.957081545064378, 0.928484848484848, 0.891005291005291, 0.986072423398329, 0.98050139275766, 0.926773455377574, 0.94047619047619, 0.960960960960961, 0.983606557377049, 0.995708154506438, 1.00253807106599, 0.967741935483871, 1.00263157894737, 1.00763358778626 ), inj42 = c(0.0238095238095238, 1, 0, 0.880952380952381, 0, 0.928571428571429, 0.857142857142857, 0, 1, 1, 0, 0, 0, 0, 0.261904761904762, 0.0714285714285714, 0.476190476190476, 0), inj14 = c(0, 1, 0, 0.785714285714286, 0, 0.785714285714286, 0.571428571428571, 0, 1, 1, 0, 0, 0, 0, 0.785714285714286, 0, 0.0714285714285714, 0)), row.names = c(NA, -18L), class = c("tbl_df", "tbl", "data.frame"))
absCA_est <- dabest(wlSNs_nobeta, group1, abs_raCA, idx=c("s", "ns")) changeCA_est <- dabest(wlSNs_nobeta, group1, change_raCA, idx=c("s", "ns")) volCA_est <- dabest(wlSNs_nobeta, group1, vol_raCA, idx=c("s", "ns"))
absCA_est_plot <- plot(absCA_est, rawplot.ylabel = "Absolute C-A", effsize.ylabel = "") changeCA_est_plot <- plot(changeCA_est, rawplot.ylabel = "Change21 C-A", effsize.ylabel = "") volCA_est_plot <- plot(volCA_est, rawplot.ylabel = "Vol21 C-A", effsize.ylabel = "") plot_grid(absCA_est_plot, changeCA_est_plot, volCA_est_plot, nrow=1, labels = "auto")
absACWR_est <- dabest(wlSNs_nobeta, group1, abs_raACWR, idx=c("s", "ns")) changeACWR_est <- dabest(wlSNs_nobeta, group1, change_raACWR, idx=c("s", "ns")) volACWR_est <- dabest(wlSNs_nobeta, group1, vol_raACWR, idx=c("s", "ns"))
absACWR_est_plot <- plot(absACWR_est, rawplot.ylabel = "Absolute ACWR", effsize.ylabel = "") changeACWR_est_plot <- plot(changeACWR_est, rawplot.ylabel = "Change21 ACWR", effsize.ylabel = "") volACWR_est_plot <- plot(volACWR_est, rawplot.ylabel = "Vol21 ACWR", effsize.ylabel = "") plot_grid(absACWR_est_plot, changeACWR_est_plot, volACWR_est_plot, nrow=1, labels = "auto")`
Hi
Was this resolved in an update?
Best,
Joseph Coyne
m | 0411 529 390 a | 18 Bondi Pl, Salt, Kingscliff NSW 2487
On 6 Sep 2019, at 12:01 pm, Joses W. Ho notifications@github.com wrote:
Closed #30 https://github.com/ACCLAB/dabestr/issues/30.
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Hi sorry, this issue has not been resolved yet. It is very curious that only the change_raACWR
column in your dataset produces a misaligned plot....
Ok understood. Any reason why you think?
Best,
Joseph Coyne
m | 0411 529 390 a | 18 Bondi Pl, Salt, Kingscliff NSW 2487
On 17 Sep 2019, at 11:27 am, Joses W. Ho notifications@github.com wrote:
Hi sorry, this issue has not been resolved yet. It is very curious that only the change_raACWR column in your dataset produces a misaligned plot....
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Hi I met the sample problem with v0.2.5. I wonder whether this problem been solved
I think the misalignment problem is due to differences of negative values. I ran on the same issue with a dataset like this:
library(dplyr)
library(dabestr)
flowering <- data.frame(
genotype = c(rep("wt", 300), rep("mutant", 100)),
anthesis = c(50 + rbinom(300, 7, 1/20), 50 + rbinom(100, 7, 1/5)),
silking = c(50 + rbinom(300, 7, 1/4), 50 + rbinom(100, 7, 3/5))
) %>%
dplyr::mutate(ASI = anthesis - silking,
SAI = silking - anthesis)
unpaired_mean_diff <- flowering %>%
dabestr::dabest(genotype, ASI,
idx = c("wt", "mutant"),
paired = FALSE) %>%
dabestr::mean_diff()
unpaired_mean_diff
plot(unpaired_mean_diff)
It disappears when I use the positive quantities:
unpaired_mean_diff <- flowering %>%
dabestr::dabest(genotype, SAI,
idx = c("wt", "mutant"),
paired = FALSE) %>%
dabestr::mean_diff()
unpaired_mean_diff
plot(unpaired_mean_diff)
Hi @faustovrz, thanks for this key bit of debugging! I'll see how to mitigate this.
Hi @josesho, you are welcome, these plots are neat, except for this bug. Any update on this issue?
@faustovrz apologies for the delay, will aim to update by end of next week!
Hi, any progress with fixing this bug? My current workaround is either to recreate the plot using ggplot from mean_diff() output or add a large positive value before computing mean_diff() and then subtract it manually from the plots using a vector manipulation software
Hi all, anyone found a solution to this? I'm using 0.3.0 and encountered the same issue with negative numbers. I have a variable whose sign is important, and thus should be conserved. Would be great to know how to fix this.
@roey-angel how did you find reproducing the plot in ggplot. Was it successful? Cheers!
@SamRPJRoss Sorry I cannot find my ggplot code right now. I mostly use my trick to convert values to positive and then subtract them in Inkscape. That's a real shame that such an important package isn't maintained.
Hi
I am having issues with the effsize.y axis. For some reason the mean and 95%CI is not aligning to the swarm plot. Please see attached screenshot and code. I have 5 other dabestr plots that I have created with other variables and they are all fine so I am unsure what is happening here. Have tried restarting R, clearing plots and environment and restarting computer.
changeACWR_est <- dabest(wlSNs_nobeta, group1, change_raACWR, idx=c("s", "ns")) changeACWR_est_plot <- plot(changeACWR_est, rawplot.ylabel = "Change21 ACWR", effsize.ylabel = "")
Any advice would be much appreciated. Thanks in advance.