Drawing Separated Shaded Areas in R Plot - r

Question

I'm trying to draw a figure of waveforms. I want to show which part of the waveforms are statistically significant. Currently, I draw a semi-transparent polygon:
plot(wave,
type = "l",
col = "red",
lwd = linewid,
pch = 19,
lty = 1,
xlab = "Time",
xaxt = "n",
xlim = c(1,duration/2),
ylab = "Difference",
ylim = c(-1, 1))
abline(h = 0)
sig <- ifelse(pval<.05,wave,0)
polygon(c(1:length(sig)),
sig,
col = rgb(1,0,0,0.5),
border = NA)
But the polygon isn't centered on the zero line of the y-axis. I'd like to shade only the areas underneath the curve of the wave. Instead, the polygon extends above the zero-line on the y-axis. Any ideas?
wave <- c(0.0484408316308237, 0.0474054439781486, 0.0467022242629086,
0.046515614318914, 0.0466686947981267, 0.0466777796491931, 0.0460966374555009,
0.0457341620230469, 0.0455045060507858, 0.0457719372614871, 0.0461446812125276,
0.0460051963987539, 0.0456347093964464, 0.0430700479769684, 0.0435837207487517,
0.0443970279017918, 0.0457508738133201, 0.0472350978374988, 0.0482361020656729,
0.0494006907171422, 0.0504508971582255, 0.0521263688769232, 0.0532433489463588,
0.0537137380543864, 0.0540428548151276, 0.0544949143122896, 0.0544225549891838,
0.0538337952743033, 0.053135984213764, 0.0523491809303349, 0.0520472332622518,
0.0517736309847163, 0.0518684887760298, 0.0514603496453925, 0.050769752723635,
0.0504389714171051, 0.0502927164308292, 0.0504354031597342, 0.0498799936275558,
0.0490825606436222, 0.0497213009991454, 0.0501938355481634, 0.0514117871384259,
0.0519380643522052, 0.0517968505801706, 0.05123157072507, 0.0520909551474945,
0.0486858357936371, 0.0493763701994425, 0.0500160784148426, 0.0505488877007248,
0.0497678090074788, 0.0480758661250716, 0.0462675525180396, 0.0453516919016191,
0.0448339366059345, 0.0445615385738649, 0.044013178561506, 0.0439648543393159,
0.0438670362724258, 0.0440913799994017, 0.0507925460506875, 0.0509727145985309,
0.0510872776847506, 0.0508104967241469, 0.0503812271559447, 0.0503631548556902,
0.0505562349708585, 0.050869650537224, 0.050115073380279, 0.0496307336460131,
0.0486946602966385, 0.0451240814629419, 0.0439636677233932, 0.0428989167765818,
0.0420026704819646, 0.0411584695778936, 0.0403788602838661, 0.040233539087147,
0.0397175149422268, 0.0389289880494877, 0.0378327839257036, 0.0360351888196015,
0.0347926091711749, 0.0341079891575494, 0.0348740749311286, 0.0349125506875405,
0.0352951033387814, 0.0344798859212136, 0.0327899391390952, 0.0303925310234825,
0.0275215845941342, 0.0265832329092289, 0.0220646495463752, 0.0122404036320984,
0.00743877530625988, 0.00181246669131438, -0.00479231506410288,
-0.0117717813867494, -0.0192370027513411, -0.027223713620762,
-0.0348613553743107, -0.0397127268587883, -0.045622681570717,
-0.0515358709254366, -0.0568288397365667, -0.0620165857779051,
-0.0669105535816898, -0.0720264470900791, -0.0766882017731929,
-0.0804427064040755, -0.0815328596670379, -0.0826051939881404,
-0.0879974600724217, -0.0924894198404777, -0.0949544486488778,
-0.104737046247734, -0.11695750473657, -0.132892205151458, -0.15164997657278,
-0.172597865364775, -0.196113512673009, -0.216646106105455, -0.244400723622597,
-0.267988695108909, -0.292598978473393, -0.317086468049069, -0.342530108945073,
-0.368486808868852, -0.399730966642985, -0.433385374917961, -0.469543692326107,
-0.507867318915593, -0.547443797215136, -0.586749203029937, -0.625603126037644,
-0.6626968183054, -0.697811797372003, -0.730226229712439, -0.760716192518167,
-0.789754092566875, -0.819837732291987, -0.844265792897494, -0.865853848085839,
-0.88772546496204, -0.908008383337203, -0.926193346905058, -0.943720637018896,
-0.958657012974673, -0.971195039738284, -0.981680462787076, -0.989209920087862,
-0.994760927508405, -0.998179967730494, -1, -0.99985631234348,
-0.998513746223383, -0.996286337260218, -0.994167673024296, -0.992029087667234,
-0.98942063019129, -0.986657143470197, -0.982080217651251, -0.97535310006632,
-0.967706563058861, -0.959931873177486, -0.953053148939477, -0.945050149326435,
-0.936863678952672, -0.927476791110897, -0.917244708485839, -0.910092208942064,
-0.898659859433262, -0.887894272800133, -0.874966302881798, -0.860464316462603,
-0.843766510522863, -0.826854760379226, -0.809030674702751, -0.790830214526396,
-0.773448702041121, -0.757822022781962, -0.742415284193991, -0.726650963278141,
-0.708671839205669, -0.690647887135473, -0.669566331925841, -0.647484673858103,
-0.625415272964118, -0.603346317669516, -0.580945690740634, -0.559174605387308,
-0.537166524153666, -0.514979755494959, -0.492190905789554, -0.4688961948937,
-0.445648845564897, -0.421370990246327, -0.394957034231288, -0.367257387362894,
-0.339759436905685, -0.31347732732076, -0.287795514335449, -0.263477496955318,
-0.240335559473844, -0.219537822868833, -0.199356394938618, -0.182724128026289,
-0.162855943390834, -0.143113588174923, -0.122168088165277, -0.100967800471397,
-0.0777710229443332, -0.0539643915465976, -0.029677750446946,
-0.00631959566058126, 0.0169258078383277, 0.0389612599575379,
0.0609770118878408, 0.0806172669927091, 0.102073705616963, 0.122665362014863,
0.142328282171209, 0.161475578433955, 0.17913203293436, 0.199700604404855,
0.216864487908698, 0.232810273813389, 0.248031682891701, 0.262732844598723,
0.276791405782004, 0.289592381780554, 0.302904563305743, 0.315933177369042,
0.331194285957781, 0.34328787498597, 0.355317635956366, 0.37161156141851,
0.385496981280364, 0.39906005718835, 0.410609126043194, 0.424557700817611,
0.432614645845991, 0.440840405298792, 0.446859449278095, 0.451067862561763,
0.454108550491332, 0.45822766032593, 0.463669025285741, 0.468751886735504,
0.477222371161998, 0.480825169330004, 0.484778309657409, 0.490686208003411,
0.496271560877119, 0.502429910894803, 0.504627189056216, 0.509277950091572,
0.512796647131139, 0.51920303298796, 0.526246371444159, 0.530172995082546,
0.537137361380815, 0.540646539738041, 0.541350429187775, 0.538037378748107,
0.53640396369579, 0.533982169384575, 0.531715003489143, 0.537771148135836,
0.541774025400292, 0.542397661260989, 0.542734418123511, 0.541900634648552,
0.551336284191385, 0.550830246001875, 0.543935588412506, 0.54850236576883,
0.546095769955119, 0.546560717106744, 0.54862072115046, 0.549873891251691,
0.549022573851835, 0.556546139368112, 0.560110491782052, 0.563328136311772,
0.556118487214394, 0.556145005611977, 0.56177222985652, 0.56211974460993,
0.563139174079545, 0.567595800986669, 0.564911164049346, 0.55370467099592,
0.549142761248365, 0.553638360274585, 0.552297050636191, 0.551520866080127,
0.545782391084414, 0.550845817729848, 0.551708815237408, 0.552680776857495,
0.560806019030281, 0.566586972251016, 0.570035930685996, 0.57778944843747,
0.575407636591647, 0.576215607600804, 0.580856907896507, 0.58111203256702,
0.580550879830819, 0.579468018580888, 0.569996133796829, 0.571472497444831,
0.570186841693214, 0.579257568699911, 0.585984875703449, 0.592864903673866,
0.592890757109184, 0.602046235792163, 0.613343736000507, 0.61690652667541,
0.615073893877543, 0.603386282668406, 0.605140483512513, 0.602317438726602,
0.601349093084652, 0.60175903066173, 0.595748856842631, 0.592466664315233,
0.579486755875179, 0.561987007946437, 0.542492099234415, 0.526383565525105,
0.5230428319822, 0.513300797695766, 0.515049254563791, 0.518848257099875,
0.506235765674015, 0.49998294091854, 0.506344856229246, 0.50475172054043,
0.507702294279798, 0.506348179486846, 0.517341319120319, 0.523551522223028,
0.530756340907612, 0.53032745351512, 0.533111198195776, 0.526453901436172,
0.529598066926201, 0.523624800099041, 0.516232193418245, 0.517039928536979,
0.501904786914197, 0.49713387651536, 0.505916234878408, 0.502395600515955,
0.489414472392961, 0.476329169842886, 0.485088777888902, 0.48219652186471,
0.469886812116599, 0.453441250799586, 0.441168281111148, 0.437074892507931,
0.438771226156789, 0.434582625256592, 0.434393831049118, 0.455313871944686,
0.46667176154786, 0.451614470975422, 0.446531804915084, 0.448747422127997,
0.442389961671837, 0.452345098594434)
pval <- structure(c(0.0237628302370617, 0.0262165284800235, 0.0285686821840486,
0.0297087853681475, 0.0299733840361694, 0.0301202024224222, 0.0323058180308351,
0.0339316553612034, 0.0381144580106053, 0.04487408115707, 0.057804021059368,
0.085158184225468, 0.136972404452296, 0.0594954230338983, 0.059815561375559,
0.0586890211651837, 0.054984325985342, 0.0505545271596015, 0.0488952044969173,
0.0471087059136155, 0.0460746356928649, 0.0424450757403614, 0.0405444189843919,
0.0411829464282132, 0.0412927140116675, 0.0417488854396546, 0.0445117370815736,
0.0550285077721912, 0.0747425914230263, 0.111097457523042, 0.15043556390993,
0.0494268999973122, 0.0517649576685409, 0.0562362352328751, 0.0608441259158306,
0.0635243703413948, 0.0648470007376663, 0.0649911512153626, 0.0678711704637943,
0.0714853336274117, 0.0656394713851027, 0.0631287997230727, 0.0691221286169588,
0.0998026839190638, 0.149978285257545, 0.195667278177658, 0.139258740157594,
0.0641286728653938, 0.0590485245121715, 0.0549751823968685, 0.0525288256855241,
0.0566756473108664, 0.0675151254516982, 0.0797001157496837, 0.0893120076127157,
0.101040948627555, 0.113937187901608, 0.136477809610576, 0.151438694370951,
0.168116109618061, 0.167693574892715, 0.055626851340157, 0.055837522780422,
0.0561583595040639, 0.0594879473890239, 0.0632759635313892, 0.065859251440062,
0.065772893740802, 0.0639366385273011, 0.0671023312185317, 0.0694330478072044,
0.0733540770931381, 0.0927895033698356, 0.0987657684863097, 0.106752925133343,
0.113783571923594, 0.121501003290016, 0.129032949168017, 0.136116836003546,
0.151762019664018, 0.175690091657166, 0.202670406948741, 0.246692883279612,
0.29427387065597, 0.339407794720914, 0.437126245014218, 0.457917873424833,
0.481184291252777, 0.523332782522114, 0.577097846183451, 0.630184174499617,
0.685063979797142, 0.719978579352288, 0.772396520583243, 0.880445896200477,
0.930819867424807, 0.983821279666508, 0.958549578396286, 0.901224976502897,
0.843510707377769, 0.785288039341357, 0.732678879305588, 0.705605278527497,
0.668649736650829, 0.632671877729848, 0.601886683772611, 0.572995378718532,
0.547203236154384, 0.522892433560929, 0.50484004632912, 0.495167623435313,
0.501651238918971, 0.508756506196948, 0.504741256872503, 0.496754657283146,
0.483869763822611, 0.453324086883336, 0.417453905522249, 0.37213400662027,
0.324969615847784, 0.279986826269611, 0.238305111925328, 0.217603724159869,
0.18615434974012, 0.165914268934125, 0.148553539851396, 0.134089539639757,
0.120930326838334, 0.108816102552138, 0.0943727175866119, 0.0809908262000654,
0.0688676027935202, 0.057965295683139, 0.0485177042268327, 0.0406774650506777,
0.0343750114181405, 0.0296041466961569, 0.0257754426846805, 0.0228491378540575,
0.0203762486696415, 0.0182050611089517, 0.0151389244136079, 0.0143291699625514,
0.0135272132937536, 0.0129494727394939, 0.0125413188392993, 0.0120654899893143,
0.0115593848885709, 0.0110971538277043, 0.0106563593895204, 0.0102594799209655,
0.00995618264115798, 0.00976027085065125, 0.00966493285702107,
0.0096809864774456, 0.00984417807568116, 0.0101140178609648,
0.0104536689988165, 0.0107455438459773, 0.0109879390786196, 0.0112476004827354,
0.0115064972197262, 0.0118436117195952, 0.012250241785758, 0.0127098856583327,
0.0131923546938643, 0.0135900513062996, 0.0140907822475909, 0.0146146781894138,
0.0153666265314495, 0.0163587611869966, 0.0165777793501283, 0.0179231032274303,
0.0193146107648153, 0.02112595949975, 0.023429090158608, 0.0263502163261689,
0.029668879819774, 0.0333886702034785, 0.0373851358797521, 0.0414244618086564,
0.0452421641298093, 0.0491730557898139, 0.0534544517392593, 0.0586659192358243,
0.0642835353988069, 0.0717515494462237, 0.0803329713593607, 0.089702211494325,
0.100024733160442, 0.111522126685171, 0.123611882298163, 0.136659951151313,
0.150762549445491, 0.166322127637489, 0.183448713985098, 0.201980927862526,
0.223096893280781, 0.248582577870016, 0.278233697709439, 0.310833681563501,
0.345332013645289, 0.382705067848975, 0.421376239222594, 0.460853428063773,
0.498027141394812, 0.535355843788925, 0.572293181350887, 0.611900790530155,
0.652931049846446, 0.698550246370366, 0.746816303915033, 0.801970397733016,
0.860682735611148, 0.922505922723998, 0.983357734959766, 0.955187832059461,
0.89653477564825, 0.837851886741715, 0.781781567273432, 0.723265191915832,
0.667546011138303, 0.614998358930736, 0.564647511026012, 0.519566323581666,
0.470697912789023, 0.432376848315165, 0.398409375708932, 0.367655920642225,
0.338940852965934, 0.312212428665514, 0.288459290398895, 0.264878592699687,
0.242704842685072, 0.217387439877778, 0.19835325593237, 0.180556517879591,
0.158171361155571, 0.141413156894301, 0.126554452518633, 0.114979049999799,
0.102918102342695, 0.0962216185484208, 0.0901194930496858, 0.0860130895609037,
0.0832340770284259, 0.0812259095628692, 0.078291162078237, 0.0742796112910293,
0.070046963535911, 0.0638805429841068, 0.0600325581294298, 0.0556731158844295,
0.0505107871259209, 0.045748968232586, 0.0409239605265858, 0.038056048177405,
0.0346897761994006, 0.0322017147611021, 0.0290191309178551, 0.0259412764702286,
0.0239876220554575, 0.0213928561132381, 0.0196012142768874, 0.0188687591178971,
0.0191111545249072, 0.0190313087419941, 0.019003849481473, 0.0188195734297014,
0.0172119066683942, 0.015771401215516, 0.0148547142814098, 0.0142875281889536,
0.0138706460080897, 0.0117612653636045, 0.0113802773390233, 0.0119929691882122,
0.011301932221071, 0.0113391829691033, 0.0111974712246918, 0.0109290980999376,
0.0105620733291735, 0.0102904702021988, 0.0088461881724392, 0.00730041492139247,
0.00668346613062251, 0.00766574212937, 0.00783946561969262, 0.00788512630201997,
0.00782058882264157, 0.00767516163055654, 0.00747564784065695,
0.00812968647923146, 0.0091908030084859, 0.00940025876764169,
0.0084452386928757, 0.00773239171673778, 0.00774262750329184,
0.00817566848920374, 0.00775737017229728, 0.00833705507967201,
0.00848219824583305, 0.00775531985314739, 0.00731753429028076,
0.00624994399211075, 0.00566319903650268, 0.00580078551643243,
0.00589284481572378, 0.00557777343775064, 0.00561015236859766,
0.00558045776809902, 0.0062741801741615, 0.00693752198709533,
0.00680148894969647, 0.00682650280136682, 0.00648353640440989,
0.00559647299682892, 0.00560310591626879, 0.00630599774150389,
0.00625849640781645, 0.00496543301213065, 0.00527106355173805,
0.00606524474497961, 0.00782669446225163, 0.00804663337329233,
0.00680216943527376, 0.00549477843115955, 0.00521495965843119,
0.00547975304067046, 0.0058083233283578, 0.00752964959779626,
0.00928425608337011, 0.0121528464847978, 0.0151204119890877,
0.0167466130623839, 0.0184702177828752, 0.0190546966808364, 0.0194217711957074,
0.0172588666752732, 0.0220542021375166, 0.0191777261144048, 0.0207814209894351,
0.0194965472902094, 0.0209260124322778, 0.0170037074001148, 0.0125849197829535,
0.0116502405937885, 0.0120529295967995, 0.0116481500418768, 0.013878269349617,
0.0138614750865797, 0.0153190475349968, 0.0194121459536112, 0.017739167396571,
0.0204726597729821, 0.0245650013533451, 0.0208055307319631, 0.0210348908355722,
0.0278106725250406, 0.035960679421438, 0.0358929798768166, 0.0405937721886476,
0.0510142810649717, 0.0561354348677331, 0.0862664430860822, 0.101130560202344,
0.111832280018731, 0.0774469081405625, 0.0813608282057401, 0.063555234011225,
0.0517641089682014, 0.0663811539378655, 0.0602507226995198, 0.0626085278234381,
0.0676820928084705, 0.0566520960018359), .Dim = c(376L, 1L))

Answer 1

The devil is always in the details with polygon vertices! Using your data from above, here is a solution and some explanation.
Get the polygon vertices, almost
sigy <- ifelse(pval < 0.05, wave, 0)
sigx <- 1:length(wave)
sigxy <- data.frame(sigx, sigy)
This is pretty much what you used in your original question. It doesn't quite work because while the polygon function accepts and connects x,y pairs, it also closes the polygon. Also, your approach was drawing a lot of polygons with zero area. So, some processing of sigxy is necessary to split it into separate polygons. This could be done manually, but it's more fun and useful to automate the process. First, remove the entries where sigy is zero. Then let's replot to see where things stand:
tmp <- sigxy[sigxy$sigy !=0,]
plot(wave, # removed some unnecessary items to simplify
type = "l",
col = "red",
xlab = "Time (by index)",
ylab = "Difference",
ylim = c(-1, 1))
abline(h = 0)
lines(tmp, col = "green")
At this point, we are much closer but are still connecting the dots and not making polygons, since we don't return to the zero line when necessary. Let's create a column that will show us where the polygons should start and stop, then gather that info into a couple of vectors of indices:
tmp$diff <- c(1, diff(tmp$sigx))
st <- 1 # start indices
end <- c() # end indices
for (i in 1:nrow(tmp)) {
if (tmp$diff[i] > 1) end <- c(end, i-1)
if ((tmp$diff[i] > 1) & (i != nrow(tmp))) st <- c(st, i)
if (i == nrow(tmp)) end <- c(end, i-1)
}
Now refresh the plot and add the polygons one at a time
plot(wave, # removed some unnecessary items to simplify
type = "l",
col = "red",
xlab = "Time (by index)",
ylab = "Difference",
ylim = c(-1, 1))
abline(h = 0)
for (i in 1:length(st)) {
DF <- tmp[st[i]:end[i], 1:2] # Just the data to be plotted
# Add the points needed to drop to the zero line
DF <- rbind(c(DF$sigx[1], 0), DF, c(DF$sigx[nrow(DF)],0))
polygon(DF, col = "green")
}
The result:

Answer 2

Bryan Hanson's solution translated into a function:
drawarea <- function(wave, pval, color){
sigy <- ifelse(pval < 0.05, wave, 0)
sigx <- 1:length(wave)
sigxy <- data.frame(sigx, sigy)
tmp <- sigxy[sigxy$sigy !=0,]
tmp$diff <- c(1, diff(tmp$sigx))
st <- 1 # start indices
end <- c() # end indices
for (i in 1:nrow(tmp)) {
if (tmp$diff[i] > 1) end <- c(end, i-1)
if ((tmp$diff[i] > 1) & (i != nrow(tmp))) st <- c(st, i)
if (i == nrow(tmp)) end <- c(end, i-1)
}
for (i in 1:length(st)){
DF <- tmp[st[i]:end[i], 1:2] # Just the data to be plotted
# Add the points needed to drop to the zero line
DF <- rbind(c(DF$sigx[1], 0), DF, c(DF$sigx[nrow(DF)],0))
polygon(DF, col = color, border=NA)
}
}