R aes function runs in R but not in r markdown

Question

I have encountered a strange problem with Markdown.

I attach hereunder the R code included in markdown for generating a correlation heatmap.

library(reshape2)
library(knitr)
library(ggplot2)
data("cars")

    # Get lower triangle of the correlation matrix
get_lower_tri<-function(cormat){
  cormat[upper.tri(cormat)] <- NA
  return(cormat)
}
# Get upper triangle of the correlation matrix
get_upper_tri <- function(cormat){
  cormat[lower.tri(cormat)]<- NA
  return(cormat)
}

reorder_cormat <- function(cormat){
  # Use correlation between variables as distance
  dd <- as.dist((1-cormat)/2)
  hc <- hclust(dd)
  cormat <-cormat[hc$order, hc$order]
}

cormat <- round(cor(cars),2)

upper_tri <- get_upper_tri(cormat)

# Reorder the correlation matrix
cormat <- reorder_cormat(cormat)

upper_tri <- get_upper_tri(cormat)

# Melt the correlation matrix
melted_cormat <- melt(upper_tri, na.rm = TRUE)

# Create a ggheatmap
ggheatmap <- ggplot(melted_cormat, aes(Var2, Var1, fill = value))+
  geom_tile(color = "white")+
  scale_fill_gradient2(low = "blue", high = "red", mid = "white", 
                       midpoint = 0, limit = c(-1,1), space = "Lab", 
                       name="Pearson\nCorrelation") +
  theme_minimal()+ # minimal theme
  theme(axis.text.x = element_text(angle = 45, vjust = 1, 
                                   size = 12, hjust = 1))+
  coord_fixed()

ggheatmap + 
  geom_text(aes(Var2, Var1, label = value), color = "black", size = 4) +
  theme(
    axis.title.x = element_blank(),
    axis.title.y = element_blank(),
    panel.grid.major = element_blank(),
    panel.border = element_blank(),
    panel.background = element_blank(),
    axis.ticks = element_blank(),
    legend.justification = c(1, 0),
    legend.position = c(0.6, 0.7),
    legend.direction = "horizontal")+
  guides(fill = guide_colorbar(barwidth = 7, barheight = 1,
                               title.position = "top", title.hjust = 0.5))

The code runs perfectly in R console but when kitted with markdown it returns this error.

Error in FUN(X[[i]], ...) : object 'Var2' not found
Calls: <Anonymous> ... by_layer -> f -> <Anonymous> -> f -> lapply -> FUN -> FUN
Execution halted

The problem seems to be in the aes function (ggplot). For some reasons it's not able to find the "Var2" present in the melt_cormap object

Any advice?

Many thanks

I don't see `Var2` defined anywhere in your sample code. Can you show where in the scope of the code it is defined? — Gary Weissman, Feb 20 '18 at 15:37
Do you have do you have library(reshape2) in your markdown code? — Vlo, Feb 20 '18 at 15:37
@GaryWeissman I don't understand your comment. Obviously, `Var2` should be a column of `melted_cormat`. — Roland, Feb 20 '18 at 15:45
Does it change smthg if you use `aes(x=Var2, y=Var1, fill = value)` ? — DJack, Feb 20 '18 at 15:49
@Roland I don't see any data here, so I can't tell what is actually in `melted_cormat` or `upper_tri` or anything else. Providing actual data with a reproducible example will often help to identify the problem. — Gary Weissman, Feb 20 '18 at 15:56
it's probably not wise to use both, but if you have to, then you should be specific with e.g. the `melt` function, i.e. `reshape2::melt` it that's the one you want — RolandASc, Feb 20 '18 at 16:07
@Roland you can use the Car dataset o the Wine one dropping the factors variables — Alberto Stefanelli, Feb 20 '18 at 16:07
@AlbertoStefanelli please see this post on creating a reproducible example, especially the section on Producing a Minimal Dataset: https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example — Gary Weissman, Feb 20 '18 at 16:10
Which `aes` call is failing? Is it the original heatmap, or when you try to add `geom_text`? — Pdubbs, Feb 20 '18 at 17:10
@AlbertoStefanelli It runs fine for me once I load all packages. As far as I know, `library` does not take multiple arguments for libraries to load. Is there an error there when you run the code in markdown? — Gary Weissman, Feb 20 '18 at 17:49

score 2 · Accepted Answer · answered Feb 20 '18 at 17:53

2

The library function does not take multiple library names as arguments although doesn't seem to throw an error. You probably have all the libraries loaded in the console, but when knitr runs it does so in a new environment and needs to load them all anew.

Try this at the top of your code:

library(reshape2) library(knitr) library(ggplot2)

If you want to load them all in a single line, there is already a SO post about that here:

Load multiple packages at once

answered Feb 20 '18 at 17:53

Gary Weissman

3,557
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1

I am using pacman as a manager. The code there reported is wrong but it just for reproducibility purposes. In any case, thanks for this, i will correct) – Alberto Stefanelli Feb 20 '18 at 23:50

score 1 · Answer 2 · answered Feb 21 '18 at 00:04

1

I resolve this, the problem was pacman. For some reason, was not loading the packages properly, I switched back to the baseline command and the issues is resolved. Thanks to everyone

answered Feb 21 '18 at 00:04

Alberto Stefanelli

310
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R aes function runs in R but not in r markdown

2 Answers2