Label every nth element in ggplot depending on row/column - r

I am plotting my PCA data (= pca.df) with ggplot (t9) and try to label my data points. With over 500 data points right next to each other, the labeling gets messy if I label every single one of them, so I want to label just every 10th or 15th data point.
I tried using gghighlight, but my basic knowledge of ifelse statements leads to no solution for me.
My code for (t9) is printed down below. The result should be a Score/Score-Plot with the values of PC1 and PC2 on the axes and every, lets say 5th element being labelled according to rownumber.
> dput(head(df))
structure(c(0.720861821444252, 0.741748310125995, 0.708402634437037,
0.709801133484984, 0.715066449559326, 0.736082130721757, 0.653704393279032,
0.698276222706427, 0.72211406630421, 0.715258352183308, 0.687541455566144,
0.70691880577236, 0.648677410108962, 0.652162185222687, 0.673335514807695,
0.686310528373139, 0.672288782506351, 0.685387769196099, 0.606520717118424,
0.591747992573417, 0.637540141146717, 0.643172972625407, 0.631438730296424,
0.684507675451748, 0.555771668718988, 0.593784695895615, 0.587382247577035,
0.576747109369824, 0.609475457932671, 0.59866246596185, 0.519063669593429,
0.530651696453032, 0.532787309576192, 0.541282412745153, 0.548262870872043,
0.538801663579734, 0.4839370855738, 0.483476075398052, 0.495569187972609,
0.508351252780073, 0.516728822566894, 0.536204665645588, 0.444866548123319,
0.451359569708855, 0.488498854129039, 0.458566775758124, 0.466211854024398,
0.491560347455407, 0.391256576032243, 0.407839446833575, 0.415186340652814,
0.424286965099726, 0.411873304932725, 0.429761415133547, 0.339836624254536,
0.368786621339532, 0.355816757014086, 0.378789270638685, 0.39335185857301,
0.391171949534279, 0.301518457021116, 0.323263419961053, 0.319326889442142,
0.329577970161398, 0.332317131236052, 0.328401547614829, 0.278194980292123,
0.271241021424707, 0.278009324614118, 0.289181065286873, 0.282708689390152,
0.287325696956387, 0.217765754577593, 0.229671138051344, 0.214270216785571,
0.248548146541018, 0.242536426938002, 0.247615674841088, 0.161232560624038,
0.167964791643414, 0.184493790352952, 0.169637631152996, 0.207171184044563,
0.18671607328531, 0.136854807157759, 0.110836224164859, 0.141700425964129,
0.170466088007464, 0.147693931044626, 0.161727182052285, 0.0820803384886784,
0.094874042231684, 0.0838404020068718, 0.106453346170999, 0.0893222925431942,
0.105425228691039, 0.0320549073043817, 0.031817899518242, 0.0492796841876071,
0.0534417407043242, 0.0492509775017762, 0.0576741314907473, -0.0003305571982993,
0.00517263223466776, 0.00898939160288738, 0.0137528774437919,
0.0152605422021288, 0.0215229583963186, -0.0532648337441121,
-0.0283369016701845, -0.0236614679612245, -0.0250738126949397,
-0.0339585310595162, -0.00502894085262935, -0.0837238471177474,
-0.0406195676958014, -0.0552223579150677, -0.0469508535844212,
-0.0427121136759291, -0.0552519953457953, -0.099633841516817,
-0.0838034423810929, -0.0891078733208937, -0.0847178896069714,
-0.0416689904316896, -0.0845884534908026, -0.112879391070739,
-0.116357070717273, -0.105954173536172, -0.0809224012272034,
-0.0803030066250538, -0.0804524938179006, -0.141076501626193,
-0.141494024691483, -0.133849678959928, -0.118385990843758, -0.113423371384572,
-0.123928162937715, -0.145978888454582, -0.145163933507897, -0.155263241214673,
-0.139704305017438, -0.119946496925743, -0.143872145220887, -0.157460920557041,
-0.172462482989155, -0.161340062935618, -0.160945553437212, -0.142106857091405,
-0.146243108149656), .Dim = c(6L, 25L), .Dimnames = list(NULL,
c("1360", "1361", "1362", "1363", "1364", "1365", "1366",
"1367", "1368", "1369", "1370", "1371", "1372", "1373", "1374",
"1375", "1376", "1377", "1378", "1379", "1380", "1381", "1382",
"1383", "1384")))
pca.df = prcomp(na.omit(df), center = FALSE)
t9 = ggplot(get_pca_var(pca.df)$coord, aes(x = get_pca_var(pca.df)$coord[,1], y = get_pca_var(pca.df)$coord[,2])) +
xlab("PC1") + ylab("PC2") +
geom_point() +
geom_text(aes(label=seq(1:nrow(get_pca_var(pca.df)$coord)), hjust=0, vjust=5))
t9
This gives the following plot, but with every element labelled:
I want some code part like this as a result, but with the ifelse or for statement (every nth row/column, for example 5th element in my "try" below) to highlight the labels:
b = as.numeric(rownames(as.data.frame(iris.pca$x)))
ggplot(iris.pca) +
geom_line(aes(x, y, colour = colour)) +
gghighlight
""(for (b in PC1) {
if (x%%5 == 0) {
print(label = as.numeric(rowname))
} else (no label)
}""
Thanks for the help!


I would have added few lines before. It is similar to your idea.
Every_Nth_label <- 5
Index <- 1
Label_full <- c(1:length(get_pca_var(pca.183s)$coord[,1]))
for(I in Label_full){
if (Index %% Every_Nth_label != 0){
Label_full[Index] <- ""
}
Index <- Index + 1
}
t9 = ggplot(get_pca_var(pca.183s)$coord,
aes(
x = get_pca_var(pca.183s)$coord[,1],
y = get_pca_var(pca.183s)$coord[,2])
) +
xlab("PC1") +
ylab("PC2") +
geom_point() +
geom_text(aes(label=Label_full, hjust=0, vjust=5))
Please let us know if this is what you wanted.

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enter image description here
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I have the following PCA plot with 7 variables (see data and code below), where I want the variable names to be put in subscript.
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0.245620918873499, 0.350757895503111, 0.314711831388176, 0.233155192989713,
0.248289747469244, 0.260316266382216, 0.435133707574921, 0.270357707406285,
0.460714026041302, 0.300202262584418, 0.283894965208827, 0.286731230742906,
0.476076636930455, 0.496419713185873, 0.449716335449948, 0.414301742272173,
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0.581232141136961, 0.388451077003248, 0.348575471498664, 0.541637601056563,
0.280529225927791, 0.474527715587717, 0.427368925204716, 0.247233045036043,
0.371205006512827, 0.350378420436755, 0.334934610173675, 0.672485054825788,
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0.905669305473566, 5.65883946946512, 2.64297457644716, 3.05508165226008,
3.18054619676744, 6.40823390030613, 3.37302493648604, 3.66350222987433,
2.54057804516827, 8.20203100920965, 2.71440979468947, 2.91087136765321,
1.99383332931126, 2.54861955298111, 2.76731871856997, 2.8168199171933,
1.87471640761942, 2.36744814319536, 2.70068269921467, 3.73984078429639,
3.14727020682767, 2.44860090082511, 2.96811391366646, 3.15924824448302,
2.75038693333045, 0.571991651163747, 0.0795687369691844, 0.199285715352744,
0.278876264579594, 0.0878147967159748, 0.776516450569034, 0.109050695318729,
0.214585168287158, 0.0733157177455723, 4.99666969059035, 0.681611322797835,
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0.00953924376517534, 0.0761805102229118, 0.06189932115376, -0.279747098684311,
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-3.38403152301908, -3.54271008856346, -5.98730765748769, -3.46145537216216,
4.08535061942786, -5.5706409165586, -5.12871207815409, -2.00980313849697,
-1.74987012389551, -4.99012113984178, -5.52220372986048, -4.09768380224705,
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9.75057146977633, 1.26769720241924, 9.92010527290404, 9.98543933499604,
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-0.771105247549713, -0.155546843451758, -0.282887876386441, -0.444554830901325,
-0.305730849504471, -0.499526713974774, -0.561585665126642, -0.731248073279858,
-0.888600847683847, -0.92906893696636, -0.32135354558875, -0.635939710773528,
-0.817948141487935, 1.6278464008073, 3.22130429296692, 3.22974945083757,
7.91888088977089, 9.00321571025501, 2.45285976212472, 6.25077115575721,
5.03100211266428, 2.74867731204381, 1.44042827261984, 5.0080717401579,
9.99481210485101, 1.47605382240812, 5.14414160776883, 7.90287723037352,
9.74082155153155, 6.49911883796255, 4.32981192308168, 8.23767292803774,
4.77091148030013, 9.32961360147844, 2.72199803938468, 3.16884732668598,
0.829324850315849, 5.05701699654261, 2.34405943658203, 3.72586945071816,
2.25735736116767, 6.09207524452358, 4.18884709620227, 3.34469041476647,
2.58207156453282, 0.749518116253117, 10.288818734698, 4.99554592402031,
12.6404861267656, 7.78458069656044, 5.22634824855874, 19.4536860734845,
18.1442198018854, 2.79630955830216, 9.58980514369905, 7.07662330872069,
2.31912315823138, 4.37504726642122, 10.6357821771254, 4.86855507971098,
15.2487045279394, 2.38136078696698, 2.2241358395045, 2.6578728514413,
2.00018415475885, 14.3105512278154, 2.79016453381628, 2.82581362407655,
3.00503022968769, 0.867751725018024, 19.840897029452, 2.76507987820854,
2.18780075665563, 2.29634886607528, 5.24806297849864, 3.00219499040395,
3.75070014856756, 4.70993515464167, 2.90138749877612, 7.88213442545384,
6.81599063475927, 2.61536476109177, 2.09377944457034, 1.96296699593464,
5.57947221212089, 5.20963124415527, 3.33875400945544, 2.79699660371989,
4.58355573223283, 1.3866287143901, 2.73741390556097, 3.83854200132191,
3.64578404258937, 8.6152262147516, 7.4471927308167, 10.7907397029921,
3.60064423537503, 2.21575071569532, 13.2584175148358, 6.69871457573026,
7.57425001679609, 10.597095658568, 6.29717063158751, 19.982005469501,
4.82507357889165, 12.0198037318264, 12.1128156222403, 0.971864601969719,
7.90290065680941, 2.69096855397026, 3.41408452807615, 3.34672867252181,
3.73752327635884, 2.59765107041846, 3.69969989638776, 6.49256678763777,
1.34200508563469, 2.58853476804991, 6.08448572133978, 2.86518771201372,
8.80958803463727, 3.21931545517097, 13.9356314451744, 3.31248219124973,
2.6213849833856, 6.81703055885931, 4.57180783512692, 0.800920105539262,
1.6915382258594, 1.97274463716894, 8.35091653894633, 4.07009290065616,
4.70143776244173, 3.73712390195578, 3.32298003757993, 2.70389301739633,
9.40504621323198, 5.22653986488779, 6.91535883117467, 4.01246708252778,
6.83368936007222, 5.52582112283756, 9.52527065730343, 5.19140504300594,
8.41044230709473, 6.70183763448149, 6.82530618272722, 9.10367484707385,
14.269079283004, 4.7895190725103, 6.59831102186193, 5.62791180796921,
6.17603897117078, 7.14836313854903, 5.96534776215752, 6.33691875052949,
4.8933652261893, 13.8731955783442, 17.7908931604276, 13.79737106661,
12.8477370319888, 1.87629146464169, 19.782149810344, 19.4288346171379,
18.9387338103106, 18.204667886657, 1.15545298295716, 19.7008843562255,
17.4563148757443, 14.7906976851945, 17.3621598140026, 1.16834398824722,
1.00026320200414, 15.0063681416214, 3.00477131232619, 5.1401701791212,
0.385864693671465, 4.36085817695906, 8.55562331421922, 5.70195167902857,
5.37442221703629, 4.73609448876232, 3.56490389804045, 5.62534291626265,
1.87125703754524, 4.91213823029151, 5.71994946518292, 5.81859005757918,
4.93084813430905, 8.53895935813586, 8.24653955462078, 5.77503573757907,
8.75251863257339, 6.42709499839693, 6.27165456948181, 6.44690599292517,
16.0425839032357, 5.03840921912342, 5.87823822697004, 4.41305622781316,
5.94650622780124, 5.56597112355133, 1.1121899643292, 5.33032094594091,
5.42635044082999, 6.6131685036545, 11.4281271025538, 6.12669843180726,
14.5658381014441, 18.4343010187149, 10.0486588804051, 19.8108604625488,
19.3252983829007, 9.68507033698261, 7.62796785042932, 14.9589012558262,
0.670023332349956, 11.1040308237076, 17.0357564882065, 1.06506975100686,
0.740390195945899), .Dim = c(96L, 7L), .Dimnames = list(NULL,
c("jd", "k1", "k2", "b1", "b2", "p1", "p2")))
and code:
library(ggbiplot)
Param.pca <- prcomp(Param.clean,scale=TRUE)
groups <- factor(c(rep("Cercis L",16),rep("Cornus L",16),rep("Ginkgo L",16),rep("Cercis R",16),rep("Cornus R",16),rep("Ginkgo R",16)))
g <- ggbiplot(Param.pca, choices=c(1,2), obs.scale = 1, var.scale = 1, ellipse.prob=0.95,
groups = groups, ellipse = TRUE, alpha=0, varname.size=6,labels.size = 10)
g <- g + geom_point(aes(shape=groups,col=groups))
g <- g + theme(legend.direction = 'vertical',
legend.position = 'right',
axis.text=element_text(size=14),axis.title=element_text(size=14),
legend.text=element_text(size=14),legend.title=element_text(size=14))
plot(g)

Following up on #RichardTelford's comment, you can get the code for ggbiplot by typing ggbiplot in your console. Then copy and paste this into a script file and assign it to a new name, say, my_ggbiplot. Then change the last if statement in the function from this:
if (var.axes) {
g <- g + geom_text(data = df.v,
aes(label = varname, x = xvar, y = yvar,
angle = angle, hjust = hjust),
color = "darkred", size = varname.size)
}
to this:
if (var.axes) {
df.v$varname = paste0(substr(df.v$varname,1,1),"[",substr(df.v$varname,2,2),"]")
g <- g + geom_text(data = df.v,
aes(label = varname, x = xvar, y = yvar,
angle = angle, hjust = hjust),
color = "darkred", size = varname.size, parse=TRUE)
}
Note the addition of the line that creates the new text labels and then the addition of parse=TRUE to geom_text. This hard-codes the labels to work specifically for your case, but you can make the function more general if you're going to do this a lot.
To run the function (once you've loaded it into your environment):
my_ggbiplot(Param.pca, choices=c(1,2), obs.scale = 1, var.scale = 1, ellipse.prob=0.95,
groups = groups, ellipse = TRUE, alpha=0, varname.size=6, labels.size = 10) +
geom_point(aes(shape=groups, col=groups)) +
theme(axis.text=element_text(size=14),
axis.title=element_text(size=14),
legend.text=element_text(size=14),
legend.title=element_text(size=14))
And here's the result:

Drawing Separated Shaded Areas in R Plot

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))

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:

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)
}
}

Add Unique Links to all Data Points in Graph with rCharts

I'm using rCharts to create a scatterplot that displays ratings that I have calculated over time. I have more information for each individual data point (rating) and would like to have each data point on the graph link to a unique page with more information about that specific data point.
For example: I would like to be able to hover over the first data point on the graph and click on it to go to a specific page (http://www.example.com/info?id=1) that provides more information about that rating or data point. Each data point has a unique id and unique url that I would like to link to.
Here is the code that I am using to generate the graph
library(rCharts)
age <- c(1:20)
tall <- seq(0.5, 1.90, length = 20)
name <- paste(letters[1:20], 1:20, sep = "")
df <- data.frame(age = age, tall = tall, name = name)
n1 <- nPlot(age ~ tall ,data = df, type = "scatterChart")
n1$xAxis(axisLabel = "the age")
n1$yAxis(axisLabel = "the tall", width = 50)
n1$chart(tooltipContent = "#! function(key, x, y, e ){
var d = e.series.values[e.pointIndex];
return 'x: ' + x + ' y: ' + y + ' name: ' + d.name
} !#")
n1

This should definitely be considered a hack for now, but it works. Issues that we face here that cause us to require this hack are the draw function in the standard rCharts template does not offer us a place to add bits of code for nvd3, and the afterScript for nvd3 falls outside of our draw so is called before the chart is rendered. Also, the nvd3 tooltip is just html, but the problem with providing a link here to click is that mouseover is triggered and the tooltip disappears before we can click on it (fun trick but not useful). So, in this hack we will hijack the tooltip content function to also specify a click event function.
I tried to be clear with comments, but please let me know if none of this makes sense. I certainly do not make a career out of support :), so I have not built up that skill set.
library(rCharts)
age <- c(1:20)
tall <- seq(0.5, 1.90, length = 20)
name <- paste(letters[1:20], 1:20, sep = "")
#this next line is not entirely necessary if other data
#provides the part of the link address
#will also comment in the js piece below to show
#how to handle that
links <- paste0("http://example.com/",name)
df <- data.frame(age = age, tall = tall, name = name, links = links)
n1 <- nPlot(age ~ tall ,data = df, type = "scatterChart")
n1$xAxis(axisLabel = "the age")
n1$yAxis(axisLabel = "the tall", width = 50)
n1$chart(tooltipContent = "#! function(key, x, y, e ){
d3.selectAll('[class*=\"nv-path\"]').on('click',function(){
//uncomment debugger if you want to see what you have
//debugger;
window.open(d3.select(this).datum().data['point'][4].links,'_blank');
//as stated in the r code generating this
//the link address might be in the data that we already have
//window.open(
// 'http://example.com/' + d3.select(this).datum().data['point'][4].name,
// '_blank'
//);
})
//looks like the actual point is below the hover tooltip path
//if tooltips disabled we could do click on the actual points
//d3.selectAll('.nv-group circle').on('click',function(){
// debugger;
//})
var d = e.series.values[e.pointIndex];
return 'x: ' + x + ' y: ' + y + ' name: ' + d.name
} !#")
n1
I hope it helps.

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