Each ggplot on separate pdf page - plot row by row [closed] - r

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I would like to put one line plot on each page of pdf file. All the data for plotting is stored in single data frame. Each row should be plotted.
That's how the data looks like:
structure(list(`10` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `34` = c(0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 370500, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1091361.9, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1512409.6,
0, 0, 0, 0, 0, 0), `59` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 4231358.2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 5995680.4, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 2266775, 0, 0, 0, 0, 0, 0, 6864490.1, 0, 0,
0, 0, 0, 0), `84` = c(0, 0, 0, 0, 1783350, 0, 0, 0, 1177650,
0, 0, 0, 0, 0, 0, 0, 0, 4316664.7, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 9262556.7, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 2831286.1, 0, 0, 0, 0, 0, 0, 10643218.2,
0, 0, 0, 0, 0, 0), `110` = c(0, 0, 0, 0, 1778743.3, 0, 0, 0,
1465966.7, 0, 0, 0, 0, 0, 0, 0, 0, 3111700, 0, 0, 1955337.5,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 5584784.4, 5584784.4,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3092525, 0,
0, 0, 0, 0, 0, 7847143.8, 0, 0, 0, 0, 0, 0), `134` = c(0, 0,
0, 0, 1121869.4, 0, 0, 0, 1439430.6, 0, 0, 0, 0, 0, 0, 0, 0,
2854250, 0, 0, 0, 0, 0, 0, 914890, 0, 0, 847880, 0, 0, 0, 0,
0, 0, 0, 8191800, 0, 0, 0, 0, 0, 0, 1830904.5, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 1650150, 0, 0, 837130, 0, 0, 0, 4925095.1, 0,
0, 0, 0, 0, 0), `165` = c(0, 0, 0, 0, 1432775, 0, 0, 0, 1394186.1,
0, 1120183.3, 0, 0, 0, 0, 0, 0, 2262421.7, 0, 0, 0, 615660, 0,
0, 1292795.8, 0, 0, 712622.5, 0, 0, 0, 0, 0, 0, 0, 2683469.4,
0, 0, 0, 0, 0, 0, 2318485.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1561800,
0, 0, 0, 0, 0, 0, 4382993.7, 0, 0, 763460, 0, 0, 0), `199` = c(0,
0, 0, 0, 1314220, 0, 0, 0, 1439718.8, 0, 1929266.7, 0, 0, 0,
1101800, 0, 0, 2759366.7, 0, 0, 0, 1291728.6, 0, 0, 2489775.6,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2858345.8, 0, 0, 0, 1819542.1,
0, 0, 1497640.3, 0, 0, 0, 1300250, 0, 0, 0, 0, 0, 0, 1566875,
0, 0, 0, 0, 0, 0, 4625895.6, 0, 0, 1308158.3, 0, 0, 0), `234` = c(1257250,
0, 0, 0, 0, 0, 0, 0, 1276080, 0, 1848500, 0, 0, 0, 1529350, 0,
0, 2155275, 0, 0, 0, 2023041.9, 0, 0, 1966447.7, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 1184200, 1184200, 0, 0, 1652350, 0, 0, 2018581.7,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1835225, 0, 0, 0, 0, 0, 0, 4639414.7,
0, 0, 720715, 0, 0, 0), `257` = c(0, 0, 0, 0, 0, 669442.5, 0,
0, 1253026.7, 0, 960410, 960410, 0, 0, 1258267.5, 0, 0, 1707392.5,
0, 0, 0, 563280, 0, 0, 2403237.9, 0, 0, 0, 1044100, 0, 2075700,
0, 0, 0, 0, 0, 5718450, 0, 0, 1704550, 0, 0, 1350286.9, 0, 0,
0, 0, 2011700, 0, 0, 0, 0, 0, 1739500, 0, 0, 0, 0, 0, 0, 4612520.8,
4612520.8, 0, 0, 0, 0, 0), `362` = c(0, 1593500, 0, 0, 0, 1610625.3,
0, 0, 1234902.5, 0, 0, 1481036.8, 0, 0, 1583647.5, 0, 0, 1752089.2,
0, 0, 0, 0, 0, 0, 2410809.2, 0, 0, 0, 654940, 0, 0, 0, 0, 0,
0, 0, 7014905.6, 0, 0, 0, 0, 0, 1165672.1, 0, 0, 0, 0, 0, 0,
0, 1029910, 0, 0, 2153087.5, 0, 0, 0, 422920, 0, 0, 0, 7495855.9,
0, 0, 0, 0, 0), `433` = c(0, 0, 0, 0, 0, 1340283.9, 0, 0, 1268996.9,
0, 0, 1416683.3, 0, 0, 1047862.5, 0, 0, 1819653.8, 0, 0, 0, 0,
0, 0, 2227565.7, 0, 0, 0, 763765, 0, 0, 1595430, 0, 0, 0, 0,
4894549, 0, 0, 0, 0, 0, 1061375.4, 0, 0, 0, 0, 0, 2251950, 0,
1042130, 0, 0, 2055300, 0, 0, 0, 696278.3, 0, 0, 0, 5353797.8,
0, 0, 0, 0, 0), `506` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2020300,
2020300, 0, 0, 0, 0, 0, 0, 7681526, 0, 0, 0, 0, 0), `581` = c(0,
0, 1749237.5, 0, 0, 0, 2421665.8, 0, 0, 1773262.5, 0, 0, 2251004.3,
0, 0, 2570175, 0, 0, 3379756.9, 0, 0, 0, 2054455.6, 0, 0, 2518270.8,
0, 0, 0, 0, 0, 0, 2917968.2, 0, 0, 0, 0, 7004350, 0, 0, 1451600,
0, 0, 1394411, 0, 0, 0, 0, 0, 2507858.3, 0, 2377012.5, 0, 0,
3719165.4, 0, 0, 0, 1472870.3, 0, 0, 9666916.1, 0, 0, 1730300,
0, 0), `652` = c(0, 0, 476910, 476910, 0, 0, 1149078.8, 1149078.8,
0, 1082468.7, 0, 0, 882769.7, 0, 0, 1370449.4, 1370449.4, 0,
1529049, 1529049, 0, 0, 943632.2, 0, 0, 916587.8, 0, 0, 0, 988261.1,
0, 0, 1778007.1, 1778007.1, 0, 0, 0, 3087304.8, 3087304.8, 0,
782860, 782860, 0, 510158.5, 510158.5, 0, 0, 0, 0, 1503750, 0,
1100677.5, 1100677.5, 0, 1669260, 1669260, 0, 0, 770733.2, 0,
0, 4939242.8, 4939242.8, 0, 643564.4, 643564.4, 0), `733` = c(0,
0, 0, 1095060, 0, 0, 0, 1674089.3, 0, 1252101.3, 0, 0, 1259111,
0, 0, 0, 2429293.3, 0, 0, 2326928.3, 0, 0, 1259216.5, 0, 0, 1238837.5,
0, 0, 0, 1224858.3, 0, 0, 0, 2952529.9, 0, 0, 0, 0, 4626414.7,
0, 0, 1121440, 0, 0, 1025386.2, 0, 0, 0, 0, 1917900, 0, 0, 2197533.3,
0, 0, 2840155.5, 0, 0, 1054285.7, 0, 0, 0, 7516814.2, 0, 0, 1329434.4,
0), `818` = c(0, 0, 0, 720551.1, 0, 0, 0, 714662.7, 0, 617012.9,
0, 0, 549850.8, 0, 0, 0, 1197460, 0, 0, 771979.2, 0, 0, 585847.5,
585847.5, 0, 875475.4, 0, 0, 0, 576774, 0, 0, 0, 1147389.8, 0,
0, 0, 0, 2292421.7, 0, 0, 755258.3, 0, 0, 0, 0, 0, 0, 0, 858930,
0, 0, 1242668.3, 0, 0, 1580088.3, 0, 0, 641938.6, 641938.6, 0,
0, 3838660.4, 0, 0, 733140.8, 733140.8), `896` = c(0, 0, 0, 590480,
0, 0, 0, 817087.6, 0, 569869.5, 0, 0, 650822.5, 650822.5, 0,
0, 1624052.5, 0, 0, 682570.8, 0, 0, 0, 1538800, 0, 690488.6,
690488.6, 0, 0, 797923.9, 0, 0, 0, 1204889.3, 0, 0, 0, 0, 2184432.2,
0, 0, 676654.7, 0, 0, 0, 210680, 0, 0, 0, 791152.5, 0, 0, 1599855.8,
0, 0, 1358543.8, 0, 0, 0, 931288, 0, 0, 4683895.2, 0, 0, 0, 1202806
), `972` = c(0, 0, 0, 799116.4, 0, 0, 0, 759169.9, 0, 408845,
0, 0, 0, 948980, 0, 0, 968766.7, 0, 0, 675349.7, 0, 0, 0, 0,
0, 0, 1811117.6, 0, 0, 609098.5, 0, 0, 0, 1073749.1, 0, 0, 0,
0, 2392258.9, 0, 0, 743580, 0, 0, 0, 1020485, 0, 0, 0, 446596.7,
0, 0, 1178583, 0, 0, 1438261.7, 0, 0, 0, 1133057.9, 0, 0, 4445814.7,
0, 0, 0, 1057776.9), `1039` = c(0, 0, 0, 447255.3, 0, 0, 0, 609409.1,
0, 304340, 0, 0, 0, 0, 0, 0, 694232.8, 0, 0, 473015.3, 0, 0,
0, 0, 0, 0, 419524.9, 0, 0, 447760.6, 0, 0, 0, 932513.5, 0, 0,
0, 0, 1251960.5, 0, 0, 276560, 0, 0, 0, 259640, 0, 0, 0, 354995,
0, 0, 1570222.5, 0, 0, 1021822, 0, 0, 0, 811614, 0, 0, 2941698.2,
0, 0, 0, 1199942.5), Gene = 1:67), .Names = c("10", "34", "59",
"84", "110", "134", "165", "199", "234", "257", "362", "433",
"506", "581", "652", "733", "818", "896", "972", "1039", "Gene"
), row.names = c(NA, 67L), class = "data.frame")
I have tried something like that so far...:
for(i in 1:nrow(Tra_decon)){
Tra_decon_melt <- melt(Tra_decon[i,], id = "Gene")
pdf("Test_plot.pdf", onefile = TRUE)
ggplot(Tra_decon_melt, aes(variable, log10(value), group=factor(Gene))) +
theme(legend.title=element_blank()) +
ylab("XXX") +
xlab("XXX") +
geom_line(aes(color=factor(Gene)), size = 1.2) +
ggtitle("XXXX") +
theme(axis.text.x = element_text(angle = 90, hjust = 1))
dev.off()
}


A solution without a for loop (and so faster) is this one:
plots <- lapply(1:nrow(Tra_decon), function(i){
Tra_decon_melt <- melt(Tra_decon[i,], id = "Gene")
ggplot(Tra_decon_melt, aes(variable, log10(value), group=factor(Gene))) +
theme(legend.title=element_blank()) +
ylab("XXX") +
xlab("XXX") +
geom_line(aes(color=factor(Gene)), size = 1.2) +
ggtitle("XXXX") +
theme(axis.text.x = element_text(angle = 90, hjust = 1))
})
pdf("Test_plot.pdf", onefile = TRUE)
plots
dev.off()


This works for me:
pdf("Test_plot.pdf", onefile = TRUE)
for(i in 1:nrow(Tra_decon)){
Tra_decon_melt <- melt(Tra_decon[i,], id.vars = "Gene")
plot<-list()
plot[[i]]<-ggplot(Tra_decon_melt, aes(variable, log10(value), group=factor(Gene))) +
theme(legend.title=element_blank()) +
ylab("XXX") +
xlab("XXX") +
geom_line(aes(color=factor(Gene)), size = 1.2) +
ggtitle("XXXX") +
theme(axis.text.x = element_text(angle = 90, hjust = 1))
print(plot[[i]])
}
dev.off()

Related

R: How can I convert list of lists data into a dataframe

I have a list of lists of matrices as shown below, I have posted the code that got me closest to my desired format and some reproducible data.
Here is picture showing the format of my data:
I would like it to be in a dataframe format, similar to that shown below:
V1 V2
1 2
1 2
1 2
1 2
1 2
1 2
The closest I got was with this code:
dt_list <- purrr::map(a, data.table::as.data.table)
dt <- data.table::rbindlist(dt_list, fill = TRUE)
But instead of putting the second list into a second row, this code adds it on to the bottom of the column.
Reproducible data:
data <- list(list(c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)), list(c(2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0)))

You can try unlist with option recursive = FALSE, e.g.,
list2DF(unlist(data, recursive = FALSE))
or use data.frame (thank #akrun's comment)
setNames(data.frame(data), paste0("V", seq_along(data)))

I think purrr::map_dfc(data, as.data.frame) may solve your problem.

ggplot with two manual color scales

I am trying to reuse some old code which I have used to make two separate plots in past, and would like to pout it together into one now.
However I have few problems
color_var <- vector(mode = "double",length = length(OP_2016$risk))
color_var[color_var== '0']<- NA
color_var[OP_2016$risk>=1 & OP_2016$risk<12] <- "yellow"
color_var[OP_2016$risk>=12] <- "red"
ggplot(OP_2016)+
geom_col(aes(x = short_date, y = risk, color = color_var , group = 1), size= 0.9) +
scale_y_continuous(limits = c(0, 100),name = "Accumulated EBHours")+
scale_color_identity("Risk Level", breaks= levels(as.factor(color_var))[c(1,2)],
labels = c("High >12 EBH","Medium 0-12EBH"),
guide = "legend"
)+
geom_line(aes(x = short_date, y= 12), linetype= "dotted", size = 0.8, colour = "red")+
# scale_color_manual("Varieties", values =c( "British Queen"= "orchid1"))+
geom_line(data = dis_fun_df, aes(x= date, y = rating, colour = "green"))
Problems:
Bars and and boxes in the legend are not filled,
I can not add manual color for geom_line and add it to the legend, that I have added from other plot.
Apologies, data set to reproduce the plot is a bit big.
dis_fun_df <- structure(list(date = structure(c(15534, 15540, 15548, 15555,
15562, 15573, 15580), class = "Date"), rating = c(10.2, 30, 61.6666666666667,
81.6666666666667, 95.8333333333333, 99.1666666666667, 100)), row.names = c(NA,
-7L), class = c("tbl_df", "tbl", "data.frame"))
OP_2016 <- structure(list(date = structure(c(1342224000, 1342227600, 1342231200,
1342234800, 1342238400, 1342242000, 1342245600, 1342249200, 1342252800,
1342256400, 1342260000, 1342263600, 1342267200, 1342270800, 1342274400,
1342278000, 1342281600, 1342285200, 1342288800, 1342292400, 1342296000,
1342299600, 1342303200, 1342306800, 1342310400, 1342314000, 1342317600,
1342321200, 1342324800, 1342328400, 1342332000, 1342335600, 1342339200,
1342342800, 1342346400, 1342350000, 1342353600, 1342357200, 1342360800,
1342364400, 1342368000, 1342371600, 1342375200, 1342378800, 1342382400,
1342386000, 1342389600, 1342393200, 1342396800, 1342400400, 1342404000,
1342407600, 1342411200, 1342414800, 1342418400, 1342422000, 1342425600,
1342429200, 1342432800, 1342436400, 1342440000, 1342443600, 1342447200,
1342450800, 1342454400, 1342458000, 1342461600, 1342465200, 1342468800,
1342472400, 1342476000, 1342479600, 1342483200, 1342486800, 1342490400,
1342494000, 1342497600, 1342501200, 1342504800, 1342508400, 1342512000,
1342515600, 1342519200, 1342522800, 1342526400, 1342530000, 1342533600,
1342537200, 1342540800, 1342544400, 1342548000, 1342551600, 1342555200,
1342558800, 1342562400, 1342566000, 1342569600, 1342573200, 1342576800,
1342580400, 1342584000, 1342587600, 1342591200, 1342594800, 1342598400,
1342602000, 1342605600, 1342609200, 1342612800, 1342616400, 1342620000,
1342623600, 1342627200, 1342630800, 1342634400, 1342638000, 1342641600,
1342645200, 1342648800, 1342652400, 1342656000, 1342659600, 1342663200,
1342666800, 1342670400, 1342674000, 1342677600, 1342681200, 1342684800,
1342688400, 1342692000, 1342695600, 1342699200, 1342702800, 1342706400,
1342710000, 1342713600, 1342717200, 1342720800, 1342724400, 1342728000,
1342731600, 1342735200, 1342738800, 1342742400, 1342746000, 1342749600,
1342753200, 1342756800, 1342760400, 1342764000, 1342767600, 1342771200,
1342774800, 1342778400, 1342782000, 1342785600, 1342789200, 1342792800,
1342796400, 1342800000, 1342803600, 1342807200, 1342810800, 1342814400,
1342818000, 1342821600, 1342825200, 1342828800, 1342832400, 1342836000,
1342839600, 1342843200, 1342846800, 1342850400, 1342854000, 1342857600,
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I think this might do the trick, using fill instead of colour
OP_2016$date <- as.Date(OP_2016$date)
color_var <- vector(mode = "double",length = length(OP_2016$risk))
color_var[color_var== '0']<- NA
color_var[OP_2016$risk>=1 & OP_2016$risk<12] <- "yellow"
color_var[OP_2016$risk>=12] <- "red"
ggplot(OP_2016)+
geom_col(aes(x = date, y = risk, group = 1,fill=color_var), size= 0.9) +
scale_y_continuous(limits = c(0, 100),name = "Accumulated EBHours")+
scale_fill_identity("Risk Level", breaks= levels(as.factor(color_var))[c(1,2)],
labels = c("High >12 EBH","Medium 0-12EBH"),
guide = "legend"
)+
geom_line(aes(x = date, y= 12), linetype= "dotted", size = 0.8, colour = "red")+
geom_line(data = dis_fun_df, aes(x= date, y = rating),colour = "green")
To my knowledge ggplot does not support multiple scales of the same type, but others would know better than I.
UPDATE:
For anyone looking to actually use multiple scales for the same type of geom the {ggnewscale} package should provide the functionality that you are looking for:
https://github.com/eliocamp/ggnewscale

Why are the number of row results always different to the number of data frame rows and how can I make them match?

I use this loop to connect to Elasticsearch, retrieve some data and add it into my data frame based on a common identifier:
library(elastic); library(jsonlite)
for (i in first_chats_eu$associate) {
firstchats_eu_body <- paste0(
'{"size":1,"query":{"bool":{"must":[{"term":{"associate":"',
i
,'"}},{"term":{"type":"conversation-archived"}}]}},"sort":{"time":"asc"}}'
)
firstchats_eu_connection <- Search(
index = "my_index",
type = "my_type",
body = firstchats_eu_body
)
first_chats_eu$firstChat[first_chats_eu$associate == i] <- fromJSON(toJSON(firstchats_eu_connection$hits$hits), flatten = TRUE)[1]$`_source.time`
}
The problem is that it always produces the following message:
Error in `$<-.data.frame`(`*tmp*`, "firstChat", value = list("2017-06-08T00:17:01.118Z", :
replacement has 445 rows, data has 446
I have looked at other answers on SO but the solutions appear to be specific to each case, and thus not applicable to mine.
What could be causing this?
If it is of any use, this loop sometimes partially succeeds, in that it returns the first 34 results and then fails for all other rows after that point.
Data frame:
structure(list(associate = c("Pm0jYumSjx", "PbjmBqnIdY", "Vq3VblKpZn",
"JUCx0MOygt", "9IxVPXPGvQ", "FUUobAsS2Z", "uflgsKMNze", "VzeedmQuiv",
"BWYbDAIPkr", "PNCzrO3TRA", "zwemlUrxQE", "y19AiLUxLN", "4hhURCoC8H",
"Ak13YJF63y", "aoQI4Ncrt4", "syaulepdzW", "ISdTwUISIG", "wncQ5pXq88",
"MYbsg1E2EQ", "OhkAz5aren", "A2wqC9F1WR", "ZDVmRyHkUY", "n5kKRmTMzj",
"mfek2ukQXk", "9Tz6HWSBTd", "b7JdFFaL7M", "TetbzmItfe", "NfCPXPfA8G",
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R plotting "Error in xy.coords(x, y)" using PerformanceAnalytics package

I'm getting error Error in xy.coords(x, y) : 'x' and 'y' lengths differ
when plotting xts object RETURNS. The plotting function used is charts.PerformanceSummary, from the package PerformanceAnalytics.
Would anyone know how to fix this? It plots regardless of the error, but the presence of an error makes conversion to HTML with knitr package fail. Interestingly running the same plotting function on a similar xts object works fine. I'm baffled.
library(PerformanceAnalytics)
# THIS PROVIDES THE ERROR:
RETURNS <- structure(c(NA, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.0176761850129417, -0.00459544547441126, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), class = c("xts", "zoo"), index = structure(c(1388448000, 1403474400, 1403475300, 1403476200, 1403477100, 1403478000, 1403478900, 1403479800, 1403480700, 1403481600, 1403482500, 1403483400, 1403484300, 1403485200, 1403486100, 1403487000, 1403487900, 1403488800, 1403489700, 1403490600, 1403491500, 1403492400, 1403493300, 1403494200, 1403495100, 1403496000, 1403496900, 1403497800, 1403498700, 1403499600, 1403500500, 1403501400, 1403502300, 1403503200, 1403504100, 1403505000, 1403505900, 1403506800, 1403507700, 1403508600, 1403509500, 1403510400, 1403511300, 1403512200, 1403513100, 1403514000, 1403514900, 1403515800, 1403516700, 1403517600, 1403518500, 1403519400, 1403520300, 1403521200, 1403522100, 1403523000, 1403523900, 1403524800, 1403525700, 1403526600, 1403527500,
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1404324900, 1404325800, 1404326700, 1404327600, 1404328500, 1404329400, 1404330300, 1404331200, 1404332100, 1404333000, 1404333900, 1404334800, 1404338400, 1404339300, 1404340200, 1404341100, 1404342000, 1404342900, 1404343800, 1404344700, 1404345600, 1404346500, 1404347400, 1404348300, 1404349200, 1404350100, 1404351000, 1404351900, 1404352800, 1404353700, 1404354600, 1404355500, 1404356400, 1404357300, 1404358200, 1404359100, 1404360000, 1404360900, 1404361800, 1404362700, 1404363600, 1404364500, 1404365400, 1404366300, 1404367200, 1404368100, 1404369000, 1404369900, 1404370800, 1404371700, 1404372600, 1404373500, 1404374400, 1404375300, 1404376200, 1404377100, 1404378000, 1404378900, 1404379800, 1404380700, 1404381600, 1404382500, 1404383400, 1404384300, 1404385200, 1404386100, 1404387000, 1404387900, 1404388800, 1404389700, 1404390600, 1404391500, 1404392400, 1404393300, 1404394200, 1404395100, 1404396000, 1404396900, 1404397800, 1404398700, 1404399600, 1404400500, 1404401400, 1404402300, 1404403200, 1404404100, 1404405000, 1404405900, 1404406800, 1404407700, 1404408600, 1404409500, 1404410400, 1404411300, 1404412200, 1404413100, 1404414000, 1404414900, 1404415800, 1404416700, 1404417600, 1404418500, 1404419400, 1404420300, 1404421200, 1404424800, 1404425700, 1404426600, 1404427500, 1404428400, 1404429300, 1404430200, 1404431100, 1404432000, 1404432900, 1404433800, 1404434700, 1404435600, 1404436500, 1404437400, 1404438300, 1404439200, 1404440100, 1404441000, 1404441900, 1404442800, 1404443700, 1404444600, 1404445500, 1404446400, 1404447300, 1404448200, 1404449100, 1404450000, 1404450900, 1404451800, 1404452700, 1404453600, 1404454500, 1404455400, 1404456300, 1404457200, 1404458100, 1404459000, 1404459900, 1404460800, 1404461700, 1404462600, 1404463500, 1404464400, 1404465300, 1404466200, 1404467100, 1404468000, 1404468900, 1404469800, 1404470700, 1404471600, 1404472500, 1404473400, 1404474300, 1404475200, 1404476100, 1404477000, 1404477900, 1404478800, 1404479700, 1404480600, 1404481500, 1404482400, 1404483300, 1404484200, 1404485100, 1404486000, 1404486900, 1404487800, 1404488700, 1404489600, 1404490500, 1404491400, 1404492300, 1404684000, 1404684900, 1404685800, 1404686700, 1404687600, 1404688500, 1404689400, 1404690300, 1404691200, 1404692100, 1404693000, 1404693900, 1404694800, 1404695700, 1404696600, 1404697500, 1404698400, 1404699300, 1404700200, 1404701100, 1404702000, 1404702900, 1404703800, 1404704700, 1404705600, 1404706500, 1404707400, 1404708300, 1404709200, 1404710100, 1404711000, 1404711900, 1404712800, 1404713700, 1404714600, 1404715500, 1404716400, 1404717300, 1404718200, 1404719100, 1404720000, 1404720900, 1404721800, 1404722700, 1404723600, 1404724500, 1404725400, 1404726300, 1404727200, 1404728100, 1404729000, 1404729900, 1404730800, 1404731700, 1404732600, 1404733500, 1404734400, 1404735300, 1404736200, 1404737100, 1404738000, 1404738900, 1404739800, 1404740700, 1404741600, 1404742500, 1404743400, 1404744300, 1404745200, 1404746100, 1404747000, 1404747900, 1404748800, 1404749700, 1404750600, 1404751500, 1404752400, 1404753300, 1404754200, 1404755100, 1404756000, 1404756900, 1404757800, 1404758700, 1404759600, 1404760500), tzone = "", tclass = c("POSIXct", "POSIXt")), .indexCLASS = c("POSIXct", "POSIXt"), .indexTZ = "", tclass = c("POSIXct", "POSIXt"), tzone = "", .Dim = c(1000L, 1L), .Dimnames = list(NULL, "End.Eq"))
charts.PerformanceSummary(RETURNS, na.rm=T)
# THIS PROVIDES NO ERROR:
RETSBYDAY <- structure(c(0, 0, 0.0131666666666667, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), index = structure(c(1403395200, 1403481600, 1403568000, 1403654400, 1403740800, 1403827200, 1.404e+09, 1404086400, 1404172800, 1404259200, 1404345600, 1404432000, 1404604800, 1404691200), tclass = "Date", tzone = "UTC"), .indexCLASS = "Date", .indexTZ = "", tclass = c("POSIXct", "POSIXt"), tzone = "", .Dim = c(14L, 1L), .Dimnames = list(NULL,"DTT3.DailyEndEq"), class = c("xts", "zoo"))
charts.PerformanceSummary(RETSBYDAY)
#RETURNS and RETSBYDAY are 1xN xts objects.
#RETURNS has an NA value and RETSBYDAY has none; including na.rm=T makes no difference.

I don't get an error using performanceanalytics version 1.4.3541. Perhaps update your version?
I do get warnings though, that "na.rm is not a graphical parameter" when calling charts.PerformanceSummary with na.rm = TRUE. This warning arises because na.rm = T is passed into the function as an extra parameter (because the function has the special parameter ...), which is then passed on to the charting functions inside charts.PerformanceSummary, which include chart.CumReturns, chart.BarVaR, and chart.Drawdown, all of which accept passthrough parameters via ... = ... in their function calls inside charts.PerformanceSummary.
You can't assume every function in R will use na.rm = TRUE to remove NAs. Just mostly base functions like mean, sum, etc... It would be safer to remove the NAs before passing data to a function, if you get errors arising from the NAs in the function call. In case you are not aware, this can usually be easily done in a one liner, such as RETURNS <- RETURNS[!is.na(RETURNS),]

Which of elements come together in different data

I'm trying to write a script to analyze my data. Would be great if you can help me with that.
Let's start with my data:
> dput(tbl_alles[1:100,])
structure(list(`10` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0), `20` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0), `52.5` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0.7306675, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0), `81` = c(0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0.91538769,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 1, 0, 0, 0), `110` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0.85441768, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0.61947266, 0, 0, 0), `140.5` = c(0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.5664111,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.6800275, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0.6300494, 0, 0, 0), `189` = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0.6234154, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0.987181, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.6194727,
0, 0, 0), `222.5` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0,
0, 1, 0, 0, 0, 0, 0, 0, 0, 0.8632862, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0.3456471, 1, 0, 0), `278` = c(0, 0, 0, 0, 0, 0, 0, 0,
0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 1, 0.61502309,
0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0.44036184, 1,
1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.42691496, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0.32234716, 0, 0, 0, 0.08890253, 0.67918373,
0, 0), `340` = c(0, 0, 0, 0, 0, 0, 0.583163048, 0, 0, 0, 0, 0,
1, 1, 0, 0, 0, 0, 1, 0.218194067, 0.325932107, 1, 0, 0, 1, 0,
0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.663889907, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0.789927058, 0, 0.44201215,
0, 0, 0, 0, 0.134339392, 0, 0.668372028, 0, 0, 0, 0, 0, 0, 0,
0.387740087, 0, 0, 0, 0, 0, 0, 0), `397` = c(0, 1, 0, 0, 0, 0,
1, 0, 1, 0, 0, 0, 0, 0.63953839, 0, 1, 0, 0, 0, 1, 1, 0.81888525,
0.89884151, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0.51459601, 0, 0, 0, 0, 0, 0, 0, 0, 1,
0, 0, 0.75141988, 0, 0, 0, 0, 0, 0, 0, 0, 0.65763553, 1, 0, 0,
0, 0, 1, 0, 1, 0.67607045, 0, 0, 0, 1, 0, 1, 1, 0, 0, 0, 1, 0,
0, 0.80260185, 0, 0, 0, 0, 0, 0, 1), `453.5` = c(0, 0.66069369,
0, 0, 0, 1, 0.57541627, 1, 1, 0, 0, 0, 1, 0.64615661, 0, 0.45209671,
0, 0, 0, 0.17022498, 0, 0, 1, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0,
0, 0, 0, 0, 0, 0.02056466, 0.08765142, 1, 0, 0, 0, 0, 0, 1, 0.53107365,
0, 0, 1, 0, 0.47454662, 1, 0.58701126, 1, 0.83194495, 0, 0, 1,
0, 0, 0, 0, 0.04550448, 0, 1, 0, 0.65763553, 1, 1, 0.05581525,
0, 0, 0.78992706, 1, 0.80859968, 0.80441503, 1, 1, 0, 0.5866736,
0, 0, 0.75623688, 0.36602167, 0, 0, 1, 0, 0.31053744, 1, 0.52549512,
1, 0, 0, 0, 0, 0.51742419), `529` = c(0, 0.521435654, 0, 0, 1,
0, 0.175996209, 0, 0, 0, 1, 0, 0, 0, 0, 0.886059888, 0, 0, 0,
0.17022498, 0, 0, 0.643526362, 0, 0, 0, 0, 0, 0.438237074, 0.01594858,
0, 0.383182117, 0, 0, 0, 0, 0, 0, 1, 0.101027654, 1, 0, 0, 0,
0, 0, 0, 0.733614607, 0.89648659, 0, 0, 0.703255538, 0, 1, 0.383200069,
0.868653232, 1, 0.065540432, 0, 0, 0.221275397, 0.229618981,
0, 0, 0, 0.14131076, 0, 0.665883882, 0, 0.399096177, 0.570186116,
0.917797708, 0.349222091, 0, 0, 0.872987981, 0, 0, 1, 1, 0.58275186,
0, 0.211497647, 0, 0, 0.929066091, 0.826799766, 0, 0, 0, 0, 0.148043509,
0.802601847, 1, 0.780383116, 0, 0, 0, 0, 0.340224249), `580` = c(0,
0.437291195, 0, 0, 1, 0, 0.20731698, 0, 0, 0, 1, 0, 0, 0, 0,
0.719755907, 0, 0, 0, 0.033248127, 0, 0, 0, 0, 0, 0, 0, 0, 0.443305568,
0, 0, 0.558877749, 0, 0, 0, 0, 0, 0, 1, 0.171621995, 1, 0, 0,
0, 0, 0, 0, 0.28952456, 1, 1, 0, 0.470920245, 0, 0.690299657,
0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0.111377617, 0.740623952, 0,
0, 0.53029633, 0, 0.917797708, 0.395559317, 0, 0, 0.484708125,
0, 0, 0.174273053, 0, 0.693355663, 0, 0.050471201, 1, 0, 0, 1,
0, 0, 0, 0, 0.698359908, 0.298609118, 0.702753583, 0.926794372,
0, 0, 0, 0, 0.320673115), `630.5` = c(0, 0.52204783, 0, 0, 0,
0, 0.48815538, 0, 0, 0, 0, 1, 0, 0, 0, 0.82709638, 0, 0, 0, 0.09539534,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0.45656691,
0.74836669, 0, 0, 0, 0, 0, 0, 0, 0.95701562, 1, 0, 0.67884433,
0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 1, 0, 1, 1, 0, 0, 0.65763553,
0, 0, 1, 0, 0, 0.77875219, 0, 0, 0.25002477, 0, 1, 0, 0, 0, 0,
0, 0.82679977, 0, 0, 0, 0, 0.84843874, 0.38138487, 0.79820877,
0, 0, 0, 0, 0, 0.51876177), `683.5` = c(0, 0.52429838, 0, 0,
0, 0, 0.59605685, 0, 0, 0, 0, 0, 0, 0, 0, 0.27845748, 0.28224351,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 1, 0, 0, 0.94942976, 0, 0, 0, 0, 0, 0.74467188, 0, 0, 0.31501511,
0, 0, 0, 0, 0, 0, 0, 0.73190143, 0, 0, 0, 0, 0, 0.90254266, 0.42921624,
0, 0, 0.56841245, 0, 0, 0.48306937, 0.54177946, 0, 0.70689046,
0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0.72875619, 0, 0, 0, 0, 1, 0.26676304,
0.77778861, 0, 0, 0, 0, 0, 0.17064527), `735.5` = c(1, 0.3768651,
0, 1, 0, 0, 0.51381348, 0, 0, 0, 0, 0, 0, 0, 0, 0.39914361, 0.22206677,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0.42663351, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.61727598,
0, 0, 0, 0, 0, 0, 0.70045244, 0, 0, 0, 0, 1, 0.62631217, 0, 0,
0, 0, 0, 0, 0.14653411, 1, 1, 0.27513455, 0, 0, 0, 0, 0.75025613,
0, 0, 0, 0, 0, 0.92484335, 0, 1, 0, 1, 0.84843874, 0.12198269,
0.58556836, 0, 0, 0, 0, 0, 0.09714178), `784` = c(0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.45656691, 0, 0, 0,
0, 0, 0, 0, 0, 1, 0, 0, 0, 0.61727598, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 1, 1, 0, 0, 0.84843874, 0, 0, 0, 0, 0, 0, 0, 0
), `832` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0.16189002, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
1, 0, 0, 0, 0, 0.2511846, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0.23427262, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0.45750616,
0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0.86974453,
1, 0, 0, 0.48180864, 0, 0, 0, 0.93083267, 0, 0, 0, 0), `882.5` = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3111616,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.63931007, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0.73948906, 0, 0, 0, 0, 0, 0, 0, 1, 0,
0, 0, 0), `926.5` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0.63485498, 0, 0, 0, 0, 0, 0, 1, 0,
0.68547559, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.35567368,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 1, 0, 0.84973396, 0, 0, 1, 0), `973` = c(0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.86100786, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0.68128251, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0.30811206, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.79599822, 0,
0, 0, 0), `1108` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0.75365872, 0, 0, 1, 0, 0, 0, 0, 0, 0.52862914,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.20061435, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0.93083267, 0, 0, 0, 0), `1200` = c(0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0,
0, 0, 0, 0, 0.67241551, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0.55638877, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)), .Names = c("10",
"20", "52.5", "81", "110", "140.5", "189", "222.5", "278", "340",
"397", "453.5", "529", "580", "630.5", "683.5", "735.5", "784",
"832", "882.5", "926.5", "973", "1108", "1200"), row.names = c("at1g01050.1",
"at1g01080.1", "at1g01090.1", "at1g01220.1", "at1g01420.1", "at1g01470.1",
"at1g01800.1", "at1g01910.5", "at1g01920.2", "at1g01980.1", "at1g02020.2",
"at1g02100.2", "at1g02130.1", "at1g02140.1", "at1g02150.1", "at1g02500.2",
"at1g02560.1", "at1g02780.1", "at1g02880.3", "at1g02920.1", "at1g02930.2",
"at1g03030.1", "at1g03110.1", "at1g03130.1", "at1g03210.1", "at1g03220.1",
"at1g03230.1", "at1g03310.2", "at1g03330.1", "at1g03475.1", "at1g03630.2",
"at1g03680.1", "at1g03870.1", "at1g03900.1", "at1g04130.1", "at1g04170.1",
"at1g04190.1", "at1g04270.2", "at1g04350.1", "at1g04410.1", "at1g04420.1",
"at1g04530.1", "at1g04640.2", "at1g04690.1", "at1g04750.2", "at1g04810.1",
"at1g04850.1", "at1g04870.2", "at1g05010.1", "at1g05180.1", "at1g05320.3",
"at1g05350.1", "at1g05520.1", "at1g05560.1", "at1g05620.2", "at1g06000.1",
"at1g06110.1", "at1g06130.2", "at1g06290.1", "at1g06410.1", "at1g06550.1",
"at1g06560.1", "at1g06570.1", "at1g06620.1", "at1g06650.2", "at1g06680.2",
"at1g06900.1", "at1g07080.1", "at1g07110.1", "at1g07140.1", "at1g07240.1",
"at1g07250.1", "at1g07440.1", "at1g07750.1", "at1g07780.4", "at1g07890.8",
"at1g07990.1", "at1g08110.3", "at1g08200.1", "at1g08360.1", "at1g08490.1",
"at1g08520.1", "at1g08550.2", "at1g08820.2", "at1g08830.2", "at1g08980.1",
"at1g09010.1", "at1g09020.1", "at1g09130.2", "at1g09210.1", "at1g09300.2",
"at1g09310.1", "at1g09340.1", "at1g09430.1", "at1g09490.2", "at1g09620.1",
"at1g09640.1", "at1g09750.1", "at1g09760.1", "at1g09780.1"), class = "data.frame")
As you can see most of cells contain a number "0".
I would like to create a subsets of my data. Let's call them "clusters". I would like to put in the same cluster "elements" (row.names) which has any value (different than 0) in the same column.
So for example:
row.name Column1 Column2 Column3 Column4
at1g02560.1 0 0.12 0 0
at1g02020.2 1 0 0.55 0.31
at1g14560.2 0.15 0.47 0 0
As you see at1g02560.1 has a value only in column 2, there is one more row which contains any value in the column 2, it's at1g14560.2. That means that they belong to the same cluster (let's say cluster 1).
The problem is that at1g02020.2 and at1g14560.2 has a value different than 0 in the column 1. They should be in the same cluster aswell (cluster 2).
In summary at1g14560.2 belong to two different clusters (cluster 1 and cluster 2).
As a result I would like to add additional column to my data named clusters and fill it with the numbers.
Example:
row.name data data data data Clusters
at1g02560.1 1
at1g14560.2 1,2
at1g02020.2 2
Is it even possible to do with R ?

Yes, it is possible to do with R. Here's one way using apply:
res <- cbind(tbl_alles,
Clusters=apply(tbl_alles, 1, function(x) paste(which(x!=0), collapse=",")))
head(res[, c(1:5, ncol(res))])
# 10 20 52.5 81 110 Clusters
# at1g01050.1 0 0 0 0 0 17
# at1g01080.1 0 0 0 0 0 11,12,13,14,15,16,17
# at1g01090.1 0 0 0 1 0 4
# at1g01220.1 0 0 0 0 0 17
# at1g01420.1 0 0 0 0 0 13,14
# at1g01470.1 0 0 0 0 0 12

You may also try:
indx <- which(!!tbl_alles,arr.ind=T)
tbl_alles$Clusters <- tapply(indx[,2],indx[,1], FUN=paste, collapse=",")
tbl_alles[1:5,c(1:5, ncol(tbl_alles))]
# 10 20 52.5 81 110 Clusters
#at1g01050.1 0 0 0 0 0 17
#at1g01080.1 0 0 0 0 0 11,12,13,14,15,16,17
#at1g01090.1 0 0 0 1 0 4
#at1g01220.1 0 0 0 0 0 17
#at1g01420.1 0 0 0 0 0 13,14

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