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Ggplot2 creates an error when used in a function or S4

I have a hard time with ggplot2 when used in a function or S4. Here is my code without function:

rm(list=ls(all=TRUE)) library(nlme) data(Oats) Data <- Oats Data$Env <- factor(Data$Block) Data$Gen <- factor(Data$Variety) Data$Gen <- factor(Data$Gen) Data$Env <- factor(Data$Env) Gen.No <- length(levels(Data$Gen)) Env.No <- length(levels(Data$Env)) Min.GE <- min(Gen.No, Env.No) GGE.ANOVA <- aov(yield ~ Env + Env:Gen, data = Data) GGE.Effs <- model.tables(GGE.ANOVA, type = "effects", cterms = "Env:Gen")$tables$"Env:Gen" SVD <- svd(GGE.Effs) D <- diag(SVD$d[1:Min.GE]) E <- SVD$u%*%sqrt(D) G <- SVD$v%*%sqrt(D) Ecolnumb <- c(1:Min.GE) Ecolnames <- paste("PC", Ecolnumb, sep="") dimnames(E) <- list(levels(Data$Env), Ecolnames) dimnames(G) <- list(levels(Data$Gen), Ecolnames) SVD.Values <- SVD$d PC.No <- c(1:length(SVD.Values)) PC.SS <- SVD.Values^2 PC.Percent.SS <- PC.SS/sum(PC.SS)*100 library(grDevices) con.hull.pos <- chull(G) con.hull <- rbind(G[con.hull.pos, ], G[con.hull.pos[1], ]) getPerpPoints <- function(mat) { x <- mat[,1] y <- mat[,2] out <- matrix(0, nrow = 2, ncol = 2) if(diff(x) == 0) { xnew <- x[1] } else { xnew <- (diff(y) / diff(x)) * x[1] - y[1] xnew <- xnew / (diff(y) / diff(x) + diff(x) / diff(y)) } ynew <- -(diff(x) / diff(y)) * xnew out[2,] <- c(xnew, ynew) return(out = out) } tmp <- t(sapply(1:(nrow(con.hull)-1), function(i) getPerpPoints(con.hull[i:(i+1),])[2, ])) tmp <- as.data.frame(tmp) library(ggplot2) r <- 0.08 p <- ggplot(data = as.data.frame(G), aes(PC1, PC2)) + geom_point() + theme_bw() p <- p + geom_text(aes(label = row.names(G)), size = 3, vjust = 1.25, colour = "black") p <- p + geom_path(data = as.data.frame(con.hull), aes(PC1, PC2)) p <- 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 <- p + geom_text(data = as.data.frame(E), aes(label = row.names(E)), size = 3, vjust = 1.35, colour = "black") p <- p + labs(list(x = sprintf("PC1 (%.1f%%)", PC.Percent.SS[1]), y = sprintf("PC2 (%.1f%%)", PC.Percent.SS[2]))) p <- p + opts(axis.title.x = theme_text(size = 10, hjust = 0.54, vjust = 0)) p <- p + opts(axis.title.y = theme_text(size = 10, angle = 90, vjust = 0.25)) p <- p + xlim(range(c(E[ ,1], G[ ,1])) + range(c(E[ ,1], G[ ,1]))*r) p <- p + ylim(range(c(E[ ,2], G[ ,2])) + range(c(E[ ,2], G[ ,2]))*r) p <- p + geom_segment(data = as.data.frame(tmp), aes(xend = tmp$V1, yend = tmp$V2), x = 0, y = 0) print(p)

and the way out is enter image description here

But when I use the same code in the following function, I got an error

 rm(list=ls(all=TRUE)) PlotGGE <- function(Response, Env, Gen, Data) { Data$Env <- factor(Data$Env) Data$Gen <- factor(Data$Gen) Gen.No <- length(levels(Data$Gen)) Env.No <- length(levels(Data$Env)) Min.GE <- min(Gen.No, Env.No) GGE.ANOVA <- aov(yield ~ Env + Env:Gen, data = Data) GGE.Effs <- model.tables(GGE.ANOVA, type = "effects", cterms = "Env:Gen")$tables$"Env:Gen" SVD <- svd(GGE.Effs) D <- diag(SVD$d[1:Min.GE]) E <- SVD$u%*%sqrt(D) G <- SVD$v%*%sqrt(D) Ecolnumb <- c(1:Min.GE) Ecolnames <- paste("PC", Ecolnumb, sep="") dimnames(E) <- list(levels(Data$Env), Ecolnames) dimnames(G) <- list(levels(Data$Gen), Ecolnames) SVD.Values <- SVD$d PC.No <- c(1:length(SVD.Values)) PC.SS <- SVD.Values^2 PC.Percent.SS <- PC.SS/sum(PC.SS)*100 library(grDevices) con.hull.pos <- chull(G) con.hull <- rbind(G[con.hull.pos, ], G[con.hull.pos[1], ]) getPerpPoints <- function(mat) { x <- mat[,1] y <- mat[,2] out <- matrix(0, nrow = 2, ncol = 2) if(diff(x) == 0) { xnew <- x[1] } else { xnew <- (diff(y) / diff(x)) * x[1] - y[1] xnew <- xnew / (diff(y) / diff(x) + diff(x) / diff(y)) } ynew <- -(diff(x) / diff(y)) * xnew out[2,] <- c(xnew, ynew) return(out = out) } tmp <- t(sapply(1:(nrow(con.hull)-1), function(i) getPerpPoints(con.hull[i:(i+1),])[2, ])) tmp <- as.data.frame(tmp) library(ggplot2) r <- 0.08 p <- ggplot(data = as.data.frame(G), aes(PC1, PC2)) + geom_point() + theme_bw() p <- p + geom_text(aes(label = row.names(G)), size = 3, vjust = 1.25, colour = "black") p <- p + geom_path(data = as.data.frame(con.hull), aes(PC1, PC2)) p <- 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 <- p + geom_text(data = as.data.frame(E), aes(label = row.names(E)), size = 3, vjust = 1.35, colour = "black") p <- p + labs(list(x = sprintf("PC1 (%.1f%%)", PC.Percent.SS[1]), y = sprintf("PC2 (%.1f%%)", PC.Percent.SS[2]))) p <- p + opts(axis.title.x = theme_text(size = 10, hjust = 0.54, vjust = 0)) p <- p + opts(axis.title.y = theme_text(size = 10, angle = 90, vjust = 0.25)) p <- p + xlim(range(c(E[ ,1], G[ ,1])) + range(c(E[ ,1], G[ ,1]))*r) p <- p + ylim(range(c(E[ ,2], G[ ,2])) + range(c(E[ ,2], G[ ,2]))*r) p <- 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)

EDIT

 Oats$Env <- factor(Oats$Block) Oats$Gen <- factor(Oats$Variety) PlotGGE(Response = yield, Env = Env, Gen = Gen, Data = Oats)

Mistake

 Error in row.names(G) : object 'G' not found

Any help and / or comments would be greatly appreciated. Thanks in advance.

-2
r ggplot2
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4 answers

Just add label columns to the data frames. Also note that you should never have $ inside aes .

This should work:

 G1 <- data.frame(G, label=rownames(G)) E1 <- data.frame(E, label=rownames(E)) library(ggplot2) r <- 0.08 p <- ggplot(data=G1, aes(PC1, PC2)) + geom_point() + theme_bw() p <- p + geom_text(aes(label=label), size=3, vjust=1.25, colour="black") p <- p + geom_path(data=as.data.frame(con.hull), aes(PC1, PC2)) p <- 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 <- p + geom_text(data=E1, aes(label=label), size=3, vjust=1.35, colour="black") p <- p + labs(list(x=sprintf("PC1 (%.1f%%)", PC.Percent.SS[1]), y=sprintf("PC2 (%.1f%%)", PC.Percent.SS[2]))) p <- p + opts(axis.title.x=theme_text(size=10, hjust=0.54, vjust=0)) p <- p + opts(axis.title.y=theme_text(size=10, angle=90, vjust=0.25)) p <- p + xlim(range(c(E[ ,1], G[ ,1])) + range(c(E[ ,1], G[ ,1]))*r) p <- p + ylim(range(c(E[ ,2], G[ ,2])) + range(c(E[ ,2], G[ ,2]))*r) p <- p + geom_segment(data=tmp, aes(xend=V1, yend=V2), x=0, y=0) print(p)
+2
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In your version, the function lacks the following two lines at the very beginning compared to the original version:

 Data$Env <- factor(Data$Block) Data$Gen <- factor(Data$Variety)

Have you experimented using debug() to execute functions to find the source of errors?

+3
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You must install as.data.frame (G) outside of your ggplot2 call if you want to use the names of the growths (G).

Set data = as.data.frame (G) in your geom_text call.

+2
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 p <- p + geom_text(aes(label = row.names(G)), size = 3, vjust = 1.25, colour = "black")

You provide it with a layer, but there is no data to build. Move label= to the original ggplot call or specify geom_text() with data= argument

0
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