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POggplot2 produces error when used in function or S4
 

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  1. POggplot2 produces error when used in function or S4
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    <p>I've tough time with ggplot2 when used in function or S4. Here is my code without function:</p> <pre><code>rm(list=ls(all=TRUE)) library(nlme) data(Oats) Data &lt;- Oats Data$Env &lt;- factor(Data$Block) Data$Gen &lt;- factor(Data$Variety) Data$Gen &lt;- factor(Data$Gen) Data$Env &lt;- factor(Data$Env) Gen.No &lt;- length(levels(Data$Gen)) Env.No &lt;- length(levels(Data$Env)) Min.G.E &lt;- min(Gen.No, Env.No) GGE.ANOVA &lt;- aov(yield ~ Env + Env:Gen, data = Data) GGE.Effs &lt;- model.tables(GGE.ANOVA, type = "effects", cterms = "Env:Gen")$tables$"Env:Gen" SVD &lt;- svd(GGE.Effs) D &lt;- diag(SVD$d[1:Min.G.E]) E &lt;- SVD$u%*%sqrt(D) G &lt;- SVD$v%*%sqrt(D) Ecolnumb &lt;- c(1:Min.G.E) Ecolnames &lt;- paste("PC", Ecolnumb, sep="") dimnames(E) &lt;- list(levels(Data$Env), Ecolnames) dimnames(G) &lt;- list(levels(Data$Gen), Ecolnames) SVD.Values &lt;- SVD$d PC.No &lt;- c(1:length(SVD.Values)) PC.SS &lt;- SVD.Values^2 PC.Percent.SS &lt;- PC.SS/sum(PC.SS)*100 library(grDevices) con.hull.pos &lt;- chull(G) con.hull &lt;- rbind(G[con.hull.pos, ], G[con.hull.pos[1], ]) getPerpPoints &lt;- function(mat) { x &lt;- mat[,1] y &lt;- mat[,2] out &lt;- matrix(0, nrow = 2, ncol = 2) if(diff(x) == 0) { xnew &lt;- x[1] } else { xnew &lt;- (diff(y) / diff(x)) * x[1] - y[1] xnew &lt;- xnew / (diff(y) / diff(x) + diff(x) / diff(y)) } ynew &lt;- -(diff(x) / diff(y)) * xnew out[2,] &lt;- c(xnew, ynew) return(out = out) } tmp &lt;- t(sapply(1:(nrow(con.hull)-1), function(i) getPerpPoints(con.hull[i:(i+1),])[2, ])) tmp &lt;- as.data.frame(tmp) library(ggplot2) r &lt;- 0.08 p &lt;- ggplot(data = as.data.frame(G), aes(PC1, PC2)) + geom_point() + theme_bw() p &lt;- p + geom_text(aes(label = row.names(G)), size = 3, vjust = 1.25, colour = "black") p &lt;- p + geom_path(data = as.data.frame(con.hull), aes(PC1, PC2)) p &lt;- p + geom_segment(data = as.data.frame(E), aes(xend = PC1, yend = PC2), x = 0, y = 0, colour = "black", arrow = arrow(angle = 25, length = unit(0.25, "cm"))) p &lt;- p + geom_text(data = as.data.frame(E), aes(label = row.names(E)), size = 3, vjust = 1.35, colour = "black") p &lt;- p + labs(list(x = sprintf("PC1 (%.1f%%)", PC.Percent.SS[1]), y = sprintf("PC2 (%.1f%%)", PC.Percent.SS[2]))) p &lt;- p + opts(axis.title.x = theme_text(size = 10, hjust = 0.54, vjust = 0)) p &lt;- p + opts(axis.title.y = theme_text(size = 10, angle = 90, vjust = 0.25)) p &lt;- p + xlim(range(c(E[ ,1], G[ ,1])) + range(c(E[ ,1], G[ ,1]))*r) p &lt;- p + ylim(range(c(E[ ,2], G[ ,2])) + range(c(E[ ,2], G[ ,2]))*r) p &lt;- p + geom_segment(data = as.data.frame(tmp), aes(xend = tmp$V1, yend = tmp$V2), x = 0, y = 0) print(p) </code></pre> <p>and the output is <img src="https://i.stack.imgur.com/jsW2V.jpg" alt="enter image description here"></p> <p>But when I use the same code in the following function, I got error</p> <pre><code>rm(list=ls(all=TRUE)) PlotGGE &lt;- function(Response, Env, Gen, Data) { Data$Env &lt;- factor(Data$Env) Data$Gen &lt;- factor(Data$Gen) Gen.No &lt;- length(levels(Data$Gen)) Env.No &lt;- length(levels(Data$Env)) Min.G.E &lt;- min(Gen.No, Env.No) GGE.ANOVA &lt;- aov(yield ~ Env + Env:Gen, data = Data) GGE.Effs &lt;- model.tables(GGE.ANOVA, type = "effects", cterms = "Env:Gen")$tables$"Env:Gen" SVD &lt;- svd(GGE.Effs) D &lt;- diag(SVD$d[1:Min.G.E]) E &lt;- SVD$u%*%sqrt(D) G &lt;- SVD$v%*%sqrt(D) Ecolnumb &lt;- c(1:Min.G.E) Ecolnames &lt;- paste("PC", Ecolnumb, sep="") dimnames(E) &lt;- list(levels(Data$Env), Ecolnames) dimnames(G) &lt;- list(levels(Data$Gen), Ecolnames) SVD.Values &lt;- SVD$d PC.No &lt;- c(1:length(SVD.Values)) PC.SS &lt;- SVD.Values^2 PC.Percent.SS &lt;- PC.SS/sum(PC.SS)*100 library(grDevices) con.hull.pos &lt;- chull(G) con.hull &lt;- rbind(G[con.hull.pos, ], G[con.hull.pos[1], ]) getPerpPoints &lt;- function(mat) { x &lt;- mat[,1] y &lt;- mat[,2] out &lt;- matrix(0, nrow = 2, ncol = 2) if(diff(x) == 0) { xnew &lt;- x[1] } else { xnew &lt;- (diff(y) / diff(x)) * x[1] - y[1] xnew &lt;- xnew / (diff(y) / diff(x) + diff(x) / diff(y)) } ynew &lt;- -(diff(x) / diff(y)) * xnew out[2,] &lt;- c(xnew, ynew) return(out = out) } tmp &lt;- t(sapply(1:(nrow(con.hull)-1), function(i) getPerpPoints(con.hull[i:(i+1),])[2, ])) tmp &lt;- as.data.frame(tmp) library(ggplot2) r &lt;- 0.08 p &lt;- ggplot(data = as.data.frame(G), aes(PC1, PC2)) + geom_point() + theme_bw() p &lt;- p + geom_text(aes(label = row.names(G)), size = 3, vjust = 1.25, colour = "black") p &lt;- p + geom_path(data = as.data.frame(con.hull), aes(PC1, PC2)) p &lt;- p + geom_segment(data = as.data.frame(E), aes(xend = PC1, yend = PC2), x = 0, y = 0, colour = "black", arrow = arrow(angle = 25, length = unit(0.25, "cm"))) p &lt;- p + geom_text(data = as.data.frame(E), aes(label = row.names(E)), size = 3, vjust = 1.35, colour = "black") p &lt;- p + labs(list(x = sprintf("PC1 (%.1f%%)", PC.Percent.SS[1]), y = sprintf("PC2 (%.1f%%)", PC.Percent.SS[2]))) p &lt;- p + opts(axis.title.x = theme_text(size = 10, hjust = 0.54, vjust = 0)) p &lt;- p + opts(axis.title.y = theme_text(size = 10, angle = 90, vjust = 0.25)) p &lt;- p + xlim(range(c(E[ ,1], G[ ,1])) + range(c(E[ ,1], G[ ,1]))*r) p &lt;- p + ylim(range(c(E[ ,2], G[ ,2])) + range(c(E[ ,2], G[ ,2]))*r) p &lt;- p + geom_segment(data = as.data.frame(tmp), aes(xend = tmp$V1, yend = tmp$V2), x = 0, y = 0) print(p) } library(nlme) data(Oats) </code></pre> <p><strong>EDIT</strong></p> <pre><code>Oats$Env &lt;- factor(Oats$Block) Oats$Gen &lt;- factor(Oats$Variety) PlotGGE(Response = yield, Env = Env, Gen = Gen, Data = Oats) </code></pre> <p>The error is </p> <pre><code>Error in row.names(G) : object 'G' not found </code></pre> <p>Any help and/or comments will be highly appreciated. Thanks in advance.</p>
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    1. COWell, your code is not the same in both instances. The first line in your `PlotGGE` function is `Data$Env <- factor(Data$Env)`. Since you pass `Oats` to your function, this is equivalent to `Oats$Env <- factor(Oats$Env)`. Since `Oats` doesn't have an `Env` column, this causes your error. This has nothing to do with `ggplot`.
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      1. USAndrie
    2. COi would not expect the very first line of your function to work as intended. Try `Data[[Env]]` instead, with `Env = "Block"`. More generally, try to debug smaller pieces at a time.
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    3. COFYI: Cross Posted, http://stats.stackexchange.com/questions/14603/ggplot2-in-function-or-s4
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      1. USBrandon Bertelsen
 

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