Find the smallest distance between the profiles - r

I would like to find the smallest distance between the profiles stored in a data frame. I am interested especially in one row in comparison to the rest of the rows stored in the data frame.
That's a data frame:
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), `34` = c(0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 393090, 0, 0, 0, 0, 0, 0, 0, 0, 0, 6718400,
0, 311350, 0), `59` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2164949.7,
4834137.6, 0, 0, 0, 1187816.7, 0, 0, 0, 0, 0, 0, 1340912.5, 0
), `84` = c(0, 0, 0, 0, 0, 0, 0, 0, 8607100, 0, 0, 17586713.2,
22629743.6, 0, 0, 0, 2808791.7, 0, 0, 4026222.5, 0, 0, 0, 1981900,
0), `110` = c(2296000, 0, 0, 0, 0, 2140221.7, 0, 0, 5809230.6,
0, 0, 37134898.5, 3861828.7, 2553100, 0, 12075845.8, 0, 0, 1272950,
8695273, 0, 0, 2657180, 2710080, 0), `134` = c(0, 0, 0, 1176150,
0, 1329596.7, 1471000, 0, 6511934, 6511934, 0, 18709227.3, 0,
1041211.2, 0, 6544176.9, 0, 0, 2412651.7, 7724956.9, 2878418.3,
0, 8620131.7, 2386972.8, 0), `165` = c(0, 1226610, 0, 1345098.7,
2083771.9, 0, 1808231.4, 0, 0, 10742997.7, 0, 13060798.9, 0,
538340, 538340, 2791649.5, 0, 0, 6217622, 1316097.1, 4716931.8,
0, 6615816.9, 1510532, 0), `199` = c(0, 1571525, 0, 1903038.3,
1676700, 0, 888832.2, 0, 0, 9084418.6, 0, 11189460.1, 0, 0, 1807662.5,
2564275, 0, 0, 18080359.7, 0, 0, 0, 2397710.2, 1717949.2, 0),
`234` = c(0, 1314900, 2482696, 1325684, 0, 0, 0, 0, 0, 7321432.7,
0, 9843409.2, 0, 0, 1073341.7, 2762775, 0, 0, 9335312.8,
0, 0, 0, 1950788.2, 1509100, 0), `257` = c(0, 1568700, 14604298.7,
940162.2, 0, 0, 0, 0, 0, 4779505.9, 0, 9691692.4, 0, 0, 735290,
2650165, 0, 2311383.7, 5193383.4, 0, 0, 0, 1341998.7, 1225325.6,
0), `362` = c(0, 0, 4190740.5, 288800, 0, 0, 0, 0, 0, 4846634.8,
0, 9574498.7, 0, 0, 0, 1425600, 0, 8339312.1, 3877892.5,
0, 0, 0, 1752866.7, 0, 0), `433` = c(0, 0, 773280, 0, 0,
0, 0, 0, 0, 3926582.8, 3926582.8, 5962586.5, 0, 0, 0, 1041400,
0, 1972909.3, 1895439.4, 0, 0, 0, 963891.2, 0, 1109800),
`506` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9332272, 0, 0, 0,
0, 0, 0, 2219100, 0, 0, 0, 0, 0, 0, 0), `581` = c(0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 4371537.1, 0, 0, 0, 0, 0, 0, 2428800,
0, 0, 0, 0, 0, 0, 0), `652` = c(0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 1689871.4, 0, 0, 0, 0, 0, 0, 988399.7, 0, 0, 0, 0, 0,
0, 0), `733` = c(0, 0, 0, 0, 0, 0, 0, 1250100, 0, 0, 1754205.3,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `818` = c(0, 0,
0, 0, 0, 0, 0, 517340, 0, 0, 1149227.6, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0), `896` = c(0, 0, 0, 0, 0, 0, 0, 579846.7,
0, 0, 985931.2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
`972` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 858255.5, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `1039` = c(0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 848993.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0)), .Names = c("10", "34", "59", "84", "110", "134",
"165", "199", "234", "257", "362", "433", "506", "581", "652",
"733", "818", "896", "972", "1039"), row.names = c("Mark_1",
"Mark_2", "Alex_1", "Katrin_1", "Georg_1", "Martin_1",
"Tim_1", "Tom_1", "Mike_1", "Mike_2", "Mike_3",
"Hare_1", "Dea_1", "Monty_1", "Monty_2", "Niko_1",
"Lee_1", "Marq_1", "Otto_1", "Priaq_1", "Surkta_1",
"Norsa_1", "Norsa_2", "Quer_1", "Quer_2"), class = "data.frame")
So the row named Katrin_1 is the one which is interesting for me. I would like to find which rows have the smallest euclidean distance to Katrin_1. Let say 3-5 rows.


Let's get rid of Katrin_1 column with df[!rownames(df) %in% "Katrin_1", ], subtract df["Katrin_1", ] from each of the remaining rows with sweep, find Euclidean distances by squaring the resulting matrix element-wise and using rowSums, use which.min to get the final result:
names(which.min(rowSums(sweep(df[!rownames(df) %in% "Katrin_1", ], 2, as.numeric(df["Katrin_1", ]), `-`)^2)))
# [1] "Mark_2"
This should be much more efficient than using dist as dist would compute all possible distances, while we need need only a few.

Related

How can I reshape the dataframe so there is only 1 observation for each id?

I need to reshape (I assume it's some sort of reshape like I would do in stata) this dataframe so that there is only 1 observation for each id. In addition, I need to preserve all of the other variables. So, one row should have columns for id, each year which contains the value of var1, x, var2 (var2 is not absolutely necessary. I've tried a lot of different things and I keep getting the same long data for the id variables. I apologize for the long dput() but there would not be information if I only did the first 6 rows.
structure(list(id= c(1806968L, 1806968L, 1806968L, 1806968L,
1806968L, 1806968L, 1806968L, 1806968L, 1806968L, 1806968L, 1806968L,
1806968L, 1806968L, 1806968L, 1806968L, 2022610L, 2022610L, 2022610L,
2022610L, 2022610L), var1 = c(0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 4877, 5819, 6560, 8262, 0, 0, 0, 0, 0), x = c(25518,
25518, 25518, 25518, 25518, 25518, 25518, 25518, 25518, 25518,
25518, 25518, 25518, 25518, 25518, 34611, 34611, 34611, 34611,
34611), var2 = c(200812L, 200912L, 201012L, 201112L, 201212L,
201312L, 201512L, 201612L, 201712L, 201812L, 201912L, 200612L,
200512L, 200712L, 201412L, 199612L, 199712L, 199812L, 199912L,
200012L), `1987` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0), `1988` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0), `1989` = c(0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `1990` = c(0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `1991` = c(0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `1992` = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `1993` = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `1994` = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `1995` = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `1996` = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `1997` = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `1998` = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `1999` = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `2000` = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `2001` = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `2002` = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `2003` = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `2004` = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `2005` = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 5819, 0, 0, 0, 0, 0, 0, 0),
`2006` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 4877, 0, 0, 0,
0, 0, 0, 0, 0), `2007` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 6560, 0, 0, 0, 0, 0, 0), `2008` = c(0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `2009` = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
`2010` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0), `2011` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0), `2012` = c(0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `2013` = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
`2014` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 8262,
0, 0, 0, 0, 0), `2015` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `2016` = c(0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `2017` = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
`2018` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0), `2019` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0), `2020` = c(0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)), row.names = c(NA,
-20L), class = c("data.table", "data.frame"), .internal.selfref = <pointer: 0x55b410de6890>, sorted = c("id",
"var1", "x", "var2"))
I would like it to look something like this, for which the value in each year is the value of var1 that corresponds with that year. Here is a something of what I want without all the years. I still need a column for all years.
id <- c(1806968L, 2022610L)
"1987" <- c(0, 8262)
x <- c(25518, 34611)
data <- data.frame(id, `1987`, x)

It's unclear whether you also want years which are 0 when x is 0. If you do, delete & var1 > 0 below.
library(tidyr)
library(dplyr)
tmp %>%
tidyr::pivot_longer(c(starts_with("1"), starts_with("2")), names_to = "year") %>%
filter(value == var1 & var1 > 0) %>%
select(-value)

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,
1342861200, 1342864800, 1342868400, 1342872000, 1342875600, 1342879200,
1342882800, 1342886400, 1342890000, 1342893600, 1342897200, 1342900800,
1342904400, 1342908000, 1342911600, 1342915200, 1342918800, 1342922400,
1342926000, 1342929600, 1342933200, 1342936800, 1342940400, 1342944000,
1342947600, 1342951200, 1342954800, 1342958400, 1342962000, 1342965600,
1342969200, 1342972800, 1342976400, 1342980000, 1342983600, 1342987200,
1342990800, 1342994400, 1342998000, 1343001600, 1343005200, 1343008800,
1343012400, 1343016000, 1343019600, 1343023200, 1343026800, 1343030400,
1343034000, 1343037600, 1343041200, 1343044800, 1343048400, 1343052000,
1343055600, 1343059200, 1343062800, 1343066400, 1343070000, 1343073600,
1343077200, 1343080800, 1343084400, 1343088000, 1343091600, 1343095200,
1343098800, 1343102400, 1343106000, 1343109600, 1343113200, 1343116800,
1343120400, 1343124000, 1343127600, 1343131200, 1343134800, 1343138400,
1343142000, 1343145600, 1343149200, 1343152800, 1343156400, 1343160000,
1343163600, 1343167200, 1343170800, 1343174400, 1343178000, 1343181600,
1343185200, 1343188800, 1343192400, 1343196000, 1343199600, 1343203200,
1343206800, 1343210400, 1343214000, 1343217600, 1343221200, 1343224800,
1343228400, 1343232000, 1343235600, 1343239200, 1343242800, 1343246400,
1343250000, 1343253600, 1343257200, 1343260800, 1343264400, 1343268000,
1343271600, 1343275200, 1343278800, 1343282400, 1343286000, 1343289600,
1343293200, 1343296800, 1343300400, 1343304000, 1343307600, 1343311200,
1343314800, 1343318400, 1343322000, 1343325600, 1343329200, 1343332800,
1343336400, 1343340000, 1343343600, 1343347200, 1343350800, 1343354400,
1343358000, 1343361600, 1343365200, 1343368800, 1343372400, 1343376000,
1343379600, 1343383200, 1343386800, 1343390400, 1343394000, 1343397600,
1343401200, 1343404800, 1343408400, 1343412000, 1343415600, 1343419200,
1343422800, 1343426400, 1343430000, 1343433600, 1343437200, 1343440800,
1343444400, 1343448000, 1343451600, 1343455200, 1343458800, 1343462400,
1343466000, 1343469600, 1343473200, 1343476800, 1343480400, 1343484000,
1343487600, 1343491200, 1343494800, 1343498400, 1343502000, 1343505600,
1343509200, 1343512800, 1343516400, 1343520000, 1343523600, 1343527200,
1343530800, 1343534400, 1343538000, 1343541600, 1343545200, 1343548800,
1343552400, 1343556000, 1343559600, 1343563200, 1343566800, 1343570400,
1343574000, 1343577600, 1343581200, 1343584800, 1343588400, 1343592000,
1343595600, 1343599200, 1343602800, 1343606400, 1343610000, 1343613600,
1343617200, 1343620800, 1343624400, 1343628000, 1343631600, 1343635200,
1343638800, 1343642400, 1343646000, 1343649600, 1343653200, 1343656800,
1343660400, 1343664000, 1343667600, 1343671200, 1343674800, 1343678400,
1343682000, 1343685600, 1343689200, 1343692800, 1343696400, 1343700000,
1343703600, 1343707200, 1343710800, 1343714400, 1343718000, 1343721600,
1343725200, 1343728800, 1343732400, 1343736000, 1343739600, 1343743200,
1343746800, 1343750400, 1343754000, 1343757600, 1343761200, 1343764800,
1343768400, 1343772000, 1343775600, 1343779200, 1343782800, 1343786400,
1343790000, 1343793600, 1343797200, 1343800800, 1343804400, 1343808000,
1343811600, 1343815200, 1343818800, 1343822400, 1343826000, 1343829600,
1343833200, 1343836800, 1343840400, 1343844000, 1343847600, 1343851200,
1343854800, 1343858400, 1343862000, 1343865600, 1343869200, 1343872800,
1343876400, 1343880000, 1343883600, 1343887200, 1343890800, 1343894400,
1343898000, 1343901600, 1343905200, 1343908800, 1343912400, 1343916000,
1343919600, 1343923200, 1343926800, 1343930400, 1343934000, 1343937600,
1343941200, 1343944800, 1343948400, 1343952000, 1343955600, 1343959200,
1343962800, 1343966400, 1343970000, 1343973600, 1343977200, 1343980800,
1343984400, 1343988000, 1343991600, 1343995200, 1343998800, 1344002400,
1344006000, 1344009600, 1344013200, 1344016800, 1344020400, 1344024000,
1344027600, 1344031200, 1344034800, 1344038400, 1344042000, 1344045600,
1344049200, 1344052800, 1344056400, 1344060000, 1344063600, 1344067200,
1344070800, 1344074400, 1344078000, 1344081600, 1344085200, 1344088800,
1344092400, 1344096000, 1344099600, 1344103200, 1344106800, 1344110400,
1344114000, 1344117600, 1344121200, 1344124800, 1344128400, 1344132000,
1344135600, 1344139200, 1344142800, 1344146400, 1344150000, 1344153600,
1344157200, 1344160800, 1344164400, 1344168000, 1344171600, 1344175200,
1344178800, 1344182400, 1344186000, 1344189600, 1344193200, 1344196800,
1344200400, 1344204000, 1344207600, 1344211200, 1344214800, 1344218400,
1344222000, 1344225600, 1344229200, 1344232800, 1344236400, 1344240000,
1344243600, 1344247200, 1344250800, 1344254400, 1344258000, 1344261600,
1344265200, 1344268800, 1344272400, 1344276000, 1344279600, 1344283200,
1344286800, 1344290400, 1344294000, 1344297600, 1344301200, 1344304800,
1344308400, 1344312000, 1344315600, 1344319200, 1344322800, 1344326400,
1344330000, 1344333600, 1344337200, 1344340800, 1344344400, 1344348000,
1344351600, 1344355200, 1344358800, 1344362400, 1344366000, 1344369600,
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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

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,
1403528400, 1403529300, 1403530200, 1403531100, 1403532000, 1403532900, 1403533800, 1403534700, 1403535600, 1403536500, 1403537400, 1403538300, 1403539200, 1403540100, 1403541000, 1403541900, 1403542800, 1403543700, 1403544600, 1403545500, 1403546400, 1403547300, 1403548200, 1403549100, 1403550000, 1403550900, 1403551800, 1403552700, 1403553600, 1403554500, 1403555400, 1403556300, 1403557200, 1403560800, 1403561700, 1403562600, 1403563500, 1403564400, 1403565300, 1403566200, 1403567100, 1403568000, 1403568900, 1403569800, 1403570700, 1403571600, 1403572500, 1403573400, 1403574300, 1403575200, 1403576100, 1403577000, 1403577900, 1403578800, 1403579700, 1403580600, 1403581500, 1403582400, 1403583300, 1403584200, 1403585100, 1403586000, 1403586900, 1403587800, 1403588700, 1403589600, 1403590500, 1403591400, 1403592300, 1403593200, 1403594100, 1403595000, 1403595900, 1403596800, 1403597700, 1403598600, 1403599500, 1403600400, 1403601300, 1403602200, 1403603100, 1403604000, 1403604900, 1403605800, 1403606700, 1403607600, 1403608500, 1403609400, 1403610300, 1403611200, 1403612100, 1403613000, 1403613900, 1403614800, 1403615700, 1403616600, 1403617500, 1403618400, 1403619300, 1403620200, 1403621100, 1403622000, 1403622900, 1403623800, 1403624700, 1403625600, 1403626500, 1403627400, 1403628300, 1403629200, 1403630100, 1403631000, 1403631900, 1403632800, 1403633700, 1403634600, 1403635500, 1403636400, 1403637300, 1403638200, 1403639100, 1403640000, 1403640900, 1403641800, 1403642700, 1403643600, 1403647200, 1403648100, 1403649000, 1403649900, 1403650800, 1403651700, 1403652600, 1403653500, 1403654400, 1403655300, 1403656200, 1403657100, 1403658000, 1403658900, 1403659800, 1403660700, 1403661600, 1403662500, 1403663400, 1403664300, 1403665200, 1403666100, 1403667000, 1403667900, 1403668800, 1403669700, 1403670600, 1403671500, 1403672400, 1403673300, 1403674200, 1403675100, 1403676000, 1403676900, 1403677800, 1403678700, 1403679600, 1403680500, 1403681400, 1403682300, 1403683200, 1403684100, 1403685000, 1403685900, 1403686800, 1403687700, 1403688600, 1403689500, 1403690400, 1403691300, 1403692200, 1403693100, 1403694000, 1403694900, 1403695800, 1403696700, 1403697600, 1403698500, 1403699400, 1403700300, 1403701200, 1403702100, 1403703000, 1403703900, 1403704800, 1403705700, 1403706600, 1403707500, 1403708400, 1403709300, 1403710200, 1403711100, 1403712000, 1403712900, 1403713800, 1403714700, 1403715600, 1403716500, 1403717400, 1403718300, 1403719200, 1403720100, 1403721000, 1403721900, 1403722800, 1403723700, 1403724600, 1403725500, 1403726400, 1403727300, 1403728200, 1403729100, 1403730000, 1403733600, 1403734500, 1403735400, 1403736300, 1403737200, 1403738100, 1403739000, 1403739900, 1403740800, 1403741700, 1403742600, 1403743500, 1403744400, 1403745300, 1403746200, 1403747100, 1403748000, 1403748900, 1403749800, 1403750700, 1403751600, 1403752500, 1403753400, 1403754300, 1403755200, 1403756100, 1403757000, 1403757900, 1403758800, 1403759700, 1403760600, 1403761500, 1403762400, 1403763300, 1403764200, 1403765100, 1403766000, 1403766900, 1403767800, 1403768700, 1403769600, 1403770500, 1403771400, 1403772300, 1403773200, 1403774100, 1403775000, 1403775900, 1403776800, 1403777700, 1403778600, 1403779500, 1403780400, 1403781300, 1403782200, 1403783100, 1403784000,
1403784900, 1403785800, 1403786700, 1403787600, 1403788500, 1403789400, 1403790300, 1403791200, 1403792100, 1403793000, 1403793900, 1403794800, 1403795700, 1403796600, 1403797500, 1403798400, 1403799300, 1403800200, 1403801100, 1403802000, 1403802900, 1403803800, 1403804700, 1403805600, 1403806500, 1403807400, 1403808300, 1403809200, 1403810100, 1403811000, 1403811900, 1403812800, 1403813700, 1403814600, 1403815500, 1403816400, 1403820000, 1403820900, 1403821800, 1403822700, 1403823600, 1403824500, 1403825400, 1403826300, 1403827200, 1403828100, 1403829000, 1403829900, 1403830800, 1403831700, 1403832600, 1403833500, 1403834400, 1403835300, 1403836200, 1403837100, 1403838000, 1403838900, 1403839800, 1403840700, 1403841600, 1403842500, 1403843400, 1403844300, 1403845200, 1403846100, 1403847000, 1403847900, 1403848800, 1403849700, 1403850600, 1403851500, 1403852400, 1403853300, 1403854200, 1403855100, 1403856000, 1403856900, 1403857800, 1403858700, 1403859600, 1403860500, 1403861400, 1403862300, 1403863200, 1403864100, 1403865000, 1403865900, 1403866800, 1403867700,
1403868600, 1403869500, 1403870400, 1403871300, 1403872200, 1403873100, 1403874000, 1403874900, 1403875800, 1403876700, 1403877600, 1403878500, 1403879400, 1403880300, 1403881200, 1403882100, 1403883000, 1403883900, 1403884800, 1403885700, 1403886600, 1403887500, 1403888400, 1403889300, 1403890200, 1403891100, 1403892000, 1403892900, 1403893800, 1403894700, 1403895600, 1403896500, 1403897400, 1403898300, 1403899200, 1403900100, 1403901000, 1403901900, 1403902800, 1404079200, 1404080100, 1404081000, 1404081900, 1404082800, 1404083700, 1404084600, 1404085500, 1404086400, 1404087300, 1404088200, 1404089100, 1404090000, 1404090900, 1404091800, 1404092700, 1404093600, 1404094500, 1404095400, 1404096300, 1404097200, 1404098100, 1404099000, 1404099900, 1404100800, 1404101700, 1404102600, 1404103500, 1404104400, 1404105300, 1404106200, 1404107100, 1404108000, 1404108900, 1404109800, 1404110700, 1404111600, 1404112500, 1404113400, 1404114300, 1404115200, 1404116100, 1404117000, 1404117900, 1404118800, 1404119700, 1404120600, 1404121500, 1404122400, 1404123300, 1404124200, 1404125100, 1404126000, 1404126900, 1404127800, 1404128700, 1404129600, 1404130500, 1404131400, 1404132300, 1404133200, 1404134100, 1404135000, 1404135900, 1404136800, 1404137700, 1404138600, 1404139500, 1404140400, 1404141300, 1404142200, 1404143100, 1404144000, 1404144900, 1404145800, 1404146700, 1404147600, 1404148500, 1404149400, 1404150300, 1404151200, 1404152100, 1404153000, 1404153900, 1404154800, 1404155700, 1404156600, 1404157500, 1404158400, 1404159300, 1404160200, 1404161100, 1404162000, 1404165600, 1404166500, 1404167400, 1404168300, 1404169200, 1404170100, 1404171000, 1404171900, 1404172800, 1404173700, 1404174600, 1404175500, 1404176400, 1404177300, 1404178200, 1404179100, 1404180000, 1404180900, 1404181800, 1404182700, 1404183600, 1404184500, 1404185400, 1404186300, 1404187200, 1404188100, 1404189000, 1404189900, 1404190800, 1404191700, 1404192600, 1404193500, 1404194400, 1404195300, 1404196200, 1404197100, 1404198000, 1404198900, 1404199800, 1404200700, 1404201600, 1404202500, 1404203400, 1404204300, 1404205200, 1404206100, 1404207000, 1404207900, 1404208800, 1404209700, 1404210600, 1404211500, 1404212400, 1404213300, 1404214200, 1404215100, 1404216000, 1404216900, 1404217800, 1404218700, 1404219600, 1404220500, 1404221400, 1404222300, 1404223200, 1404224100, 1404225000, 1404225900, 1404226800, 1404227700, 1404228600, 1404229500, 1404230400, 1404231300, 1404232200, 1404233100, 1404234000, 1404234900, 1404235800, 1404236700, 1404237600, 1404238500, 1404239400, 1404240300, 1404241200, 1404242100, 1404243000, 1404243900, 1404244800, 1404245700, 1404246600, 1404247500, 1404248400, 1404252000, 1404252900, 1404253800, 1404254700, 1404255600, 1404256500, 1404257400, 1404258300, 1404259200, 1404260100, 1404261000, 1404261900, 1404262800, 1404263700, 1404264600, 1404265500, 1404266400, 1404267300, 1404268200, 1404269100, 1404270000, 1404270900, 1404271800, 1404272700, 1404273600, 1404274500, 1404275400, 1404276300, 1404277200, 1404278100, 1404279000, 1404279900, 1404280800, 1404281700, 1404282600, 1404283500, 1404284400, 1404285300, 1404286200, 1404287100, 1404288000, 1404288900, 1404289800, 1404290700, 1404291600, 1404292500, 1404293400, 1404294300, 1404295200, 1404296100, 1404297000, 1404297900, 1404298800, 1404299700, 1404300600, 1404301500, 1404302400, 1404303300, 1404304200, 1404305100, 1404306000, 1404306900, 1404307800, 1404308700, 1404309600, 1404310500, 1404311400, 1404312300, 1404313200, 1404314100, 1404315000, 1404315900, 1404316800, 1404317700, 1404318600, 1404319500, 1404320400, 1404321300, 1404322200, 1404323100, 1404324000,
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),]

Subset rows with similar strings in one of the column and plot them together

I would like to group/subset the rows which have the same "base" string in one of the column and plot them on one graph. It would be great to have everything in one pdf file.. Each graph on separate page of pdf.
Data:
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 = c("AT1G04170_1", "AT1G04170_2", "AT1G04170_3",
"AT1G04170_4", "AT1G08520_1", "AT1G08520_2", "AT1G08520_3", "AT1G08520_4",
"AT1G10670_1", "AT1G10670_2", "AT1G53500_1", "AT1G53500_2", "AT1G53500_3",
"AT1G53500_4", "AT1G54270_1", "AT1G54270_2", "AT1G54270_3", "AT1G80480_1",
"AT1G80480_2", "AT1G80480_3", "AT2G16950_1", "AT2G16950_2", "AT2G16950_3",
"AT2G16950_4", "AT3G03960_1", "AT3G03960_2", "AT3G03960_3", "AT3G57290_1",
"AT3G57290_2", "AT3G57290_3", "AT3G63460_1", "AT3G63460_2", "AT3G63460_3",
"AT3G63460_4", "AT4G20890_1", "AT4G20890_2", "AT4G20890_3", "AT4G20890_4",
"AT4G20890_5", "AT4G20980_1", "AT4G20980_2", "AT4G20980_3", "AT4G24190_1",
"AT4G24190_2", "AT4G24190_3", "AT4G24190_4", "AT4G29670_1", "AT4G29670_2",
"AT4G29670_3", "AT4G29670_4", "AT5G23740_1", "AT5G23740_2", "AT5G23740_3",
"AT5G23860_1", "AT5G23860_2", "AT5G23860_3", "AT5G40450_1", "AT5G40450_2",
"AT5G40450_3", "AT5G40450_4", "AT5G62700_1", "AT5G62700_2", "AT5G62700_3",
"ATCG00780_1", "ATCG00780_2", "ATCG00780_3", "ATCG00780_4")), .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("AT1G04170_1", "AT1G04170_2", "AT1G04170_3",
"AT1G04170_4", "AT1G08520_1", "AT1G08520_2", "AT1G08520_3", "AT1G08520_4",
"AT1G10670_1", "AT1G10670_2", "AT1G53500_1", "AT1G53500_2", "AT1G53500_3",
"AT1G53500_4", "AT1G54270_1", "AT1G54270_2", "AT1G54270_3", "AT1G80480_1",
"AT1G80480_2", "AT1G80480_3", "AT2G16950_1", "AT2G16950_2", "AT2G16950_3",
"AT2G16950_4", "AT3G03960_1", "AT3G03960_2", "AT3G03960_3", "AT3G57290_1",
"AT3G57290_2", "AT3G57290_3", "AT3G63460_1", "AT3G63460_2", "AT3G63460_3",
"AT3G63460_4", "AT4G20890_1", "AT4G20890_2", "AT4G20890_3", "AT4G20890_4",
"AT4G20890_5", "AT4G20980_1", "AT4G20980_2", "AT4G20980_3", "AT4G24190_1",
"AT4G24190_2", "AT4G24190_3", "AT4G24190_4", "AT4G29670_1", "AT4G29670_2",
"AT4G29670_3", "AT4G29670_4", "AT5G23740_1", "AT5G23740_2", "AT5G23740_3",
"AT5G23860_1", "AT5G23860_2", "AT5G23860_3", "AT5G40450_1", "AT5G40450_2",
"AT5G40450_3", "AT5G40450_4", "AT5G62700_1", "AT5G62700_2", "AT5G62700_3",
"ATCG00780_1", "ATCG00780_2", "ATCG00780_3", "ATCG00780_4"), class = "data.frame")
I would like to subset rows with the same "basis" which means string before dash.
I was trying to combine subset and grep function but it works for me only if I give the string manually. It would be quite a lot of work do to it string by string.

You could gather() your data into long format, separate() the Gene column into label and number and, for better plot aesthetics, replace the 0 values with NAs in the y column using na_if() and specify the order of the x axis using factor()
library(dplyr)
library(tidyr)
long_df <- df %>%
gather(x, y, -Gene) %>%
separate(Gene, into = c("label", "number")) %>%
mutate(y = na_if(y, 0),
x = factor(x, levels = unique(x)))
Then, based on this answer, you could create the plot p and iterate through the groups using dplyr's do() or purrr's by_slice()
library(ggplot2)
p = ggplot(data = long_df, aes(x = x, y = y, color = number)) + geom_point()
# Using dplyr's do()
res <- long_df %>%
group_by(label) %>%
do(plots = p %+% . + facet_wrap(~label))
# Using purrr's by_slice()
library(purrr)
res <- long_df %>%
slice_rows("label") %>%
by_slice(~(p %+% . + facet_wrap(~label)), .to = "plots")
Which gives:
#Source: local data frame [19 x 2]
#Groups: <by row>
#
## A tibble: 19 × 2
# label plots
#* <chr> <list>
#1 AT1G04170 <S3: gg>
#2 AT1G08520 <S3: gg>
#3 AT1G10670 <S3: gg>
#4 AT1G53500 <S3: gg>
#5 AT1G54270 <S3: gg>
#6 AT1G80480 <S3: gg>
#7 AT2G16950 <S3: gg>
#8 AT3G03960 <S3: gg>
#9 AT3G57290 <S3: gg>
#10 AT3G63460 <S3: gg>
#11 AT4G20890 <S3: gg>
#12 AT4G20980 <S3: gg>
#13 AT4G24190 <S3: gg>
#14 AT4G29670 <S3: gg>
#15 AT5G23740 <S3: gg>
#16 AT5G23860 <S3: gg>
#17 AT5G40450 <S3: gg>
#18 AT5G62700 <S3: gg>
#19 ATCG00780 <S3: gg>
You can then access each plot, for example:
res$plots[1]
Which gives:
To save all plots into a pdf, simply do:
pdf()
res$plots
dev.off()

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

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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()

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