Hi Arun, thank you very much. That code worked perfectly.

Below is the full version of the code with the addition of a legend. 

Irucka


rm(list=ls())
source("read.funkyfile.R")
temp = read.funkyfile("seasonalFluxComparisonDataSet.csv", "station_id",
header=TRUE, sep="\t")
temp1<-lapply(temp,function(x) {x1<-x[,colSums(is.na(x))!=nrow(x)];
if(is.data.frame(x1)) x1[complete.cases(x1),] else
x1[complete.cases(x1)] })
# temp1<-lapply(temp1,function(x) x[is.data.frame(x)])

#3 columns subset
temp3<-temp1[lapply(temp1,length)==3]

temp3New<-temp3[sapply(temp3,is.data.frame)]
pdf("Calibration_Results/Nitrogen/Graphics/seasonalFluxComparisonDataSet
full.pdf")
lapply(names(temp3New),function(i) {x<-temp3New[[i]];
matplot(x[,1],x[,-1],type="n",lty=1,sub=i,main="Seasonal Flux Sum",
xlab="Calendar Year Timesteps",ylab="Total Flux (kg/season)");
matlines(x[,1],x[,-1],type="l",lty=1:2,lwd=1,col=1:2);
legend("topright", inset=.05, title="Seasonal Flux Methods", lty=c(1,1),
col= c("black", "red"), c("EGRET/WRTDS","Fluxmaster"), horiz=TRUE)})
dev.off()

#2 columns subset
temp2<-temp1[lapply(temp1,length)==2]
temp2New<-lapply(temp2,function(x) lapply(names(x)[-1], function(i)
{x1<-cbind(x[,1],x[,i]);colnames(x1)<- c("Month",i);x1} ))

pdf("Calibration_Results/Nitrogen/Graphics/seasonalFluxComparisonDataSet
partial.pdf")
par(mfrow=c(1,1))
lapply(names(temp2New),function(i) lapply(temp2New[[i]],function(x)
{plot(x[,1],x[,2],main="Seasonal Flux
Sum",sub=paste(i,colnames(x)[2],sep=" "),xlab="Calendar Year
Timesteps",ylab="Total Flux (kg/season)");lines(x[,1],x[,2])}))
dev.off()


<-----Original Message-----> 
>From: arun [smartpink111@yahoo.com]
>Sent: 3/29/2013 4:47:57 PM
>To: iruckaE@mail2world.com
>Cc: r-help@r-project.org
>Subject: Re: [R] multiple plots and looping assistance requested
(single plot)
>
>
>
>HI Irucka,
>
>Please check this:
>temp<- structure(list(`:Bostoncitydata` = structure(list(Month = c(1L,
>2L, 3L, NA), Data1 = c(1.5, 12.3, 11.4, NA), Data2 = c(9.1342,
>12.31, 3.5, NA)), .Names = c("Month", "Data1", "Data2"), class =
"data.frame", row.names = c(NA,
>-4L)), `:Chicagocitydata` = structure(list(Month = c(1L, 2L,
>3L, 4L, 5L, NA), Data1 = c(1.52, 12.63, 20.34, 12.83, 3.34, NA
>), Data2 = c(19.41342, 13.031, 0.80021, 12.63104, 19.20021, NA
>)), .Names = c("Month", "Data1", "Data2"), class = "data.frame",
row.names = c(NA,
>-6L)), `:NewYorkcitydata` = structure(list(Month = c(1L, 2L,
>3L, 4L, 5L, 6L, 7L, NA), Data1 = c(NA, NA, NA, NA, NA, NA, NA,
>NA), Data2 = c(3.1342, 1.31, 13.5, 1.31, 2.40021, 0.25, 26.3,
>NA)), .Names = c("Month", "Data1", "Data2"), class = "data.frame",
row.names = c(NA,
>-8L)), `:Philadelphiacitydata` = structure(list(Month = c(1L,
>2L, 3L, 4L, 5L, 6L, NA), Data1 = c(1.65, 11.63, 5.0434, 13.73,
>3.0234, 34.209, NA), Data2 = c(2.61342, 16.331, 19.040021, 17.831,
>10.1010021, 3.80742, NA)), .Names = c("Month", "Data1", "Data2"
>), class = "data.frame", row.names = c(NA, -7L)), `:Atlantacitydata` =
structure(list(
>Month = c(1L, 2L, 3L, NA), Data1 = c(NA, NA, NA, NA), Data2 = c(NA,
>NA, NA, NA)), .Names = c("Month", "Data1", "Data2"), class =
"data.frame", row.names = c(NA,
>-4L)), `:Baltimorecitydata` = structure(list(Month = 1:2, Data1 =
c(11.325,
>32.433), Data2 = c(49.71342, 52.4031)), .Names = c("Month", "Data1",
>"Data2"), class = "data.frame", row.names = c(NA, -2L))), .Names =
c(":Bostoncitydata",
>":Chicagocitydata", ":NewYorkcitydata", ":Philadelphiacitydata",
>":Atlantacitydata", ":Baltimorecitydata")) 
>
>
>temp1<-lapply(temp,function(x) {x1<-x[,colSums(is.na(x))!=nrow(x)];
if(is.data.frame(x1)) 
>x1[complete.cases(x1),] else x1[complete.cases(x1)] })
># temp1<-lapply(temp1,function(x) x[is.data.frame(x)])
>#3 columns subset
>temp3<-temp1[lapply(temp1,length)==3]
>
>
>temp3New<-temp3[sapply(temp3,is.data.frame)]
>pdf("Irucka.pdf")
>lapply(names(temp3New),function(i) {x<-temp3New[[i]];
matplot(x[,1],x[,-
>1],type="n",lty=1,sub=i,main="Seasonal Flux Sum", xlab="Calendar Year
Timesteps",ylab="Total Flux 
>(kg/season)"); matlines(x[,1],x[,-1],type="l",lty=1:2,lwd=1,col=1:2)})
>dev.off()
>
>A.K.
>
>
>
>________________________________
>From: Irucka Embry <iruckaE@mail2world.com>
>To: smartpink111@yahoo.com 
>Sent: Friday, March 29, 2013 5:41 PM
>Subject: Re: [R] multiple plots and looping assistance requested
(single plot)
>
>
>Hi Arun, I'm sorry about the data not being read correctly. 
>
>OK, thank you so much!
>
>Irucka
>
>
><-----Original Message-----> 
>>From: arun [smartpink111@yahoo.com]
>>Sent: 3/29/2013 3:36:21 PM
>>To: iruckaE@mail2world.com
>>Subject: Re: [R] multiple plots and looping assistance requested
(single plot)
>>
>>HI Irucka,
>>No problem. Thanks for the dput(data), but it seems like the data is
not read correctly. It still has comma 
>>as separator.
>>
>>str(temp)
>>List of 5
>> $ 02143500,,:'data.frame': 17 obs. of 1 variable:
>> ..$ CYEAR_Decimal.load_00600_W.load_00600_F: Factor w/ 17 levels
",,","2000.875,,4202.7437226",..: 
>2 
>>3 4 5 6 7 8 9 10 11 ...
>> $ 02169000,,:'data.frame': 17 obs. of 1 variable:
>> ..$ CYEAR_Decimal.load_00600_W.load_00600_F: Factor w/ 17 levels
",,","2000.875,,227675.73764",..: 
>2 
>>3 4 5 6 7 8 9 10 11 ...
>> $ 02169500,,:'data.frame': 17 obs. of 1 variable:
>> ..$ CYEAR_Decimal.load_00600_W.load_00600_F: Factor w/ 17 levels
",,","2000.875,,414312.49534",..: 
>2 
>>3 4 5 6 7 8 9 10 11 ....
>> $ 02169570,,:'data.frame': 17 obs. of 1 variable:
>> ..$ CYEAR_Decimal.load_00600_W.load_00600_F: Factor w/ 17 levels 
>>",,","2000.875,2897.79043403356,5155.6776796",..: 2 3 4 5 6 7 8 9 10
11 ...
>> $ 02172300,,:'data.frame': 12 obs. of 1 variable:
>> ..$ CYEAR_Decimal.load_00600_W.load_00600_F: Factor w/ 12 levels
"2001.875,,899.46439731",..: 1 2 
>3 
>>4 5 6 7 8 9 10 ...
>>
>>
>>I actually found the dataset containing Bostoncitydata, etc.. I will
work on that.
>>
>>
>>
>>________________________________
>> From: Irucka Embry <iruckaE@mail2world.com>
>>To: smartpink111@yahoo.com 
>>Sent: Friday, March 29, 2013 1:35 PM
>>Subject: Re: [R] multiple plots and looping assistance requested
(single plot)
>> 
>>
>>Hi Arun, that is fine. 
>>
>>I want to thank you in advance for your assistance.
>>
>>Irucka
>>
>>
>><-----Original Message-----> 
>>>From: arun [smartpink111@yahoo.com]
>>>Sent: 3/29/2013 10:02:35 AM
>>>To: iruckaE@mail2world.com
>>>Subject: Re: [R] multiple plots and looping assistance requested
(single plot)
>>>
>>>Will look into it later. 
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>From: Irucka Embry <iruckaE@mail2world.com>
>>>To: smartpink111@yahoo.com 
>>>Sent: Friday, March 29, 2013 11:02 AM
>>>Subject: Re: [R] multiple plots and looping assistance requested
(single plot)
>>>
>>>
>>>
>>>Hi Arun, how are you?
>>>
>>>Thank you for the response. Yes, I would like to have the xy scatter
plot with connecting lines for both 
>>>columns to be in the same plot window. 
>>>
>>>I'm sorry that I forgot the data, but it is included below.
>>>
>>>dput(temp)
>>>structure(list(`02143500,,` =
structure(list(CYEAR_Decimal.load_00600_W.load_00600_F = 
>>structure(c(2L, 
>>>3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 
>>>17L, 1L), .Label = c(",,", "2000.875,,4202.7437226",
"2001.125,,16214.840538", 
>>>"2001.375,,7371.9290209", "2001.625,,3114.1090754",
"2001.875,,2464.1114951", 
>>>"2002.125,,9380.6352081", "2002.375,,3859.2809055",
"2002.625,,901.86146915", 
>>>"2002.875,,22377.413599", "2003.125,,53563.26564",
"2003.375,,148264.35049", 
>>>"2003.625,,103538.36278", "2003.875,,18142.045363",
"2004.125,,14672.031667", 
>>>"2004.375,,18796.93618", "2004.625,,75313.330193"), class =
"factor")), .Names = 
>>>"CYEAR_Decimal.load_00600_W..load_00600_F", class = "data.frame",
row..names = c(NA, 
>>>-17L)), `02169000,,` =
structure(list(CYEAR_Decimal.load_00600_W.load_00600_F = structure(c(2L,
>>>3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 
>>>17L, 1L), .Label = c(",,", "2000.875,,227675.73764",
"2001.125,,92777.682029", 
>>>"2001.375,,84827.680295", "2001..625,,193298.65669",
"2001.875,,170799.05034", 
>>>"2002.125,,103666.8759", "2002.375,,107485.71333",
"2002.625,,213765.87505", 
>>>"2002.875,,472307.65662", "2003.125,,799500.99994",
"2003.375,,754868..43185", 
>>>"2003.625,,454078.02653", "2003.875,,171521.77777",
"2004.125,,265827.90007", 
>>>"2004.375,,120401.25989", "2004.625,,194000.26057"), class =
"factor")), .Names = 
>>>"CYEAR_Decimal.load_00600_W.load_00600_F", class = "data.frame",
row.names = c(NA, 
>>>-17L)), `02169500,,` =
structure(list(CYEAR_Decimal.load_00600_W.load_00600_F = structure(c(2L,
>>>3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 
>>>17L, 1L), .Label = c(",,", "2000.875,,414312.49534",
"2001.125,,617213.70273", 
>>>"2001.375,,434832.6564", "2001.625,,388556.44724",
"2001.875,,349308.46381", 
>>>"2002.125,,633838.70254", "2002.375,,384887.09244",
"2002.625,,303766.12561", 
>>>"2002.875,,1065566.5203", "2003.125,,2156874..9757",
"2003.375,,2521072.5523", 
>>>"2003.625,,1377743.9361", "2003.875,,683078.62134",
"2004.125,,936362.89268", 
>>>"2004.375,,625201.60587", "2004.625,,1094215.7135"), class =
"factor")), .Names = 
>>>"CYEAR_Decimal.load_00600_W.load_00600_F", class = "data..frame",
row.names = c(NA, 
>>>-17L)), `02169570,,` =
structure(list(CYEAR_Decimal.load_00600_W.load_00600_F = structure(c(2L,
>>>3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 
>>>17L, 1L), .Label = c(",,", "2000.875,2897.79043403356,5155.6776796", 
>>>"2001.125,7551.09451122126,10514.485482",
"2001.375,4062.39365601964,5937.0104684", 
>>>"2001.625,4386.39358258187,8642..4433388",
"2001.875,2148.48034139629,2018.779571", 
>>>"2002.125,5887.51583868203,6126.7033234",
"2002.375,4551.71006202726,5345.9677373", 
>>>"2002.625,5159.07068303165,6881.9457464",
"2002.875,10946.0644606408,10500.817808", 
>>>"2003.125,20223.5133431944,16945.048319",
"2003.375,14275.7834627696,15041.816646", 
>>>"2003.625,16653.6617307992,17141.673609",
"2003.875,13901.0420234613,8335.6620592", 
>>>"2004.125,13396.5350817751,7485.3528412",
"2004.375,10918.1025781646,7429.6229871", 
>>>"2004.625,37343..1840220637,15796.869042"), class = "factor")),
.Names = 
>>>"CYEAR_Decimal..load_00600_W.load_00600_F", class = "data.frame",
row.names = c(NA, 
>>>-17L)), `02172300,,` =
structure(list(CYEAR_Decimal.load_00600_W.load_00600_F = structure(1:12,
>>>.Label = c("2001.875,,899.46439731", 
>>>"2002.125,,1667.869248", "2002.375,,952.12246929",
"2002.625,,543.12231908", 
>>>"2002.875,,1663.8731209", "2003.125,,3123.5771201",
"2003.375,,4338..1307758", 
>>>"2003.625,,4469.2046052", "2003.875,,2642.983822",
"2004.125,,2863.529214", 
>>>"2004.375,,2131.6573312", "2004.625,,2476.4154125"), class =
"factor")), .Names = 
>>>"CYEAR_Decimal.load_00600_W.load_00600_F", class = "data.frame",
row.names = c(NA, 
>>>-12L))), .Names = c("02143500,,", "02169000,,", "02169500,,", 
>>>"02169570,,", "02172300,,"))
>>>
>>>
>>>Irucka
>>>
>>>
>>><-----Original Message-----> 
>>>>From: arun [smartpink111@yahoo.com]
>>>>Sent: 3/29/2013 6:02:22 AM
>>>>To: iruckaE@mail2world.com
>>>>Subject: Re: [R] multiple plots and looping assistance requested
(single plot)
>>>>
>>>>HI Irucka,
>>>>
>>>>Could you send me the data? Lots of emails, so it is difficult to
search your previous email (I also 
>>>deleted 
>>>>all emails from my inbox recently).
>>>>
>>>>By single plot means you wanted them in the same plot window, right?
>>>>
>>>>
>>>>
>>>>________________________________
>>>> From: Irucka Embry <iruckaE@mail2world.com>
>>>>To: smartpink111@yahoo.com 
>>>>Sent: Friday, March 29, 2013 3:50 AM
>>>>Subject: Re: [R] multiple plots and looping assistance requested
(single plot)
>>>> 
>>>>
>>>>Hi Arun, how are you?
>>>>
>>>>A couple of weeks ago you assisted me by drafting the following code
for me. This code prints 
>>the 
>>>>contents of the 3 columns subset in two different plots. Is it
possible to print the contents of the 3 
>>>>columns subset in one single plot? If so, then how would that be
done?
>>>>
>>>>I would like to thank you in advance.
>>>>
>>>>Irucka Embry
>>>>
>>>>
>>>>
>>>>temp = read..funkyfile("seasonalFluxComparisonDataSet.csv",
"station_id", header=TRUE, 
>>sep="\t")
>>>>temp1<-lapply(temp,function(x) {x1<-x[,colSums(is.na(x))!=nrow(x)];
if(is.data.frame(x1)) 
>>>>x1[complete..cases(x1),] else x1[complete.cases(x1)]})
>>>># temp1<-lapply(temp1,function(x) x[is.data.frame(x)])
>>>>
>>>>#3 columns subset
>>>>temp3<-temp1[lapply(temp1,length)==3]
>>>>temp3New<-lapply(temp3,function(x) lapply(names(x)[-1], function(i)
{x1<-
>>>>cbind(x[,1],x[,i]);colnames(x1)<- c("Month",i);x1} ))
>>>>pdf("seasonalFluxComparisonDataSetfull.pdf")
>>>>par(mfrow=c(1,1))
>>>>lapply(names(temp3New),function(i) lapply(temp3New[[i]],function(x) 
>>{plot(x[,1],x[,2],main="Seasonal 
>>>>Flux Sum",sub=paste(i,colnames(x)[2],sep=" "),xlab="Calendar Year
Timesteps",ylab="Total Flux 
>>>>(kg/season)");lines(x[,1],x[,2])}))
>>>>dev.off()
>>>>
>>>>#2 columns subset
>>>>temp2<-temp1[lapply(temp1,length)==2]
>>>>temp2New<-lapply(temp2,function(x) lapply(names(x)[-1], function(i)
{x1<-
>>>>cbind(x[,1],x[,i]);colnames(x1)<- c("Month",i);x1} ))
>>>>
>>>>pdf("seasonalFluxComparisonDataSetpartial.pdf")
>>>>par(mfrow=c(1,1))
>>>>lapply(names(temp2New),function(i) lapply(temp2New[[i]],function(x) 
>>{plot(x[,1],x[,2],main="Seasonal 
>>>>Flux Sum",sub=paste(i,colnames(x)[2],sep=" "),xlab="Calendar Year
Timesteps",ylab="Total Flux 
>>>>(kg/season)");lines(x[,1],x[,2])}))
>>>>dev.off() 


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