Plotting missing values using ggplot2

Question

I am trying to plot missing values using the function below. I get this error message:

Don't know how to automatically pick scale for object of type data.frame. Defaulting to continuous.
Error: Aesthetics must be either length 1 or the same as the data (65507): fill, x, y'

library(reshape2)
library(ggplot2)
library(dplyr)

ggplot_missing <- function(x){

  x %>% 
    is.na %>%
    melt %>%
    ggplot(data = .,
           aes(x ,
               y )) +
geom_raster(aes(fill = value)) +
    scale_fill_grey(name = "",
                    labels = c("Present","Missing")) +
    theme_minimal() + 
    theme(axis.text.x  = element_text(angle=45, vjust=0.5)) + 
    labs(x = "Variables in Dataset",
         y = "Rows / observations")
} 

ggplot_missing(productholding)

Any ideas?

the error message says it - the length of vector value needs to be either 1 (all obs same value) or same as length of the series. Have a look if the df is correctly melted... — Jan Sila
– Jan Sila, Commented Aug 23, 2017 at 7:37
If you provide a reproducible example it will be easier for others to help you. — elevendollar
– elevendollar, Commented Aug 23, 2017 at 7:42

Adam Quek · Accepted Answer · 2017-08-23 08:20:45Z

3

The x and y in the ggplot is not specified in your function. I changed it to the following:

ggplot_missing <- function(data){
  df2 <- data %>% is.na %>% melt 

  ggplot(df2, aes(Var2, Var1, fill=value)) + 
    geom_raster() + 
    scale_fill_grey(name="", labels=c("Present", "Missing")) +
    theme_minimal() + 
    theme(axis.text.x  = element_text(angle=45, vjust=0.5)) + 
    labs(x = "Variables in Dataset",
         y = "Rows / observations")
}

Test data:

df <- iris
set.seed(4)
df[sample(nrow(df), 20), 2] <- NA
df[sample(nrow(df), 30), 3] <- NA
df[sample(nrow(df), 15), 4] <- NA

ggplot_missing(df)

edited Aug 23, 2017 at 8:20

answered Aug 23, 2017 at 8:06

Adam Quek

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2 Comments

Que Over a year ago

Thank you so much :-). This helps.

Rio Over a year ago

what is var2 and var1? I get an error not finding these variables!

Brian D · Accepted Answer · 2017-12-15 16:13:14Z

Slight variation on OP's question. If you want to visualize the missing data pattern for each variable at different levels of another (factor) variable...

ggplot_missing2 <- function(data, xvar, yvars) {
  # xvar should be a factor variable for this to work
  require(ggplot2)
  require(reshape2)
  newvar = "variable"
  newval = "value"
  dl <- melt(data, id.vars = xvar, measure.vars=yvars, variable.name=newvar, value.name = newval)
  dl <- dcast(dl, formula = as.formula(paste0(newvar,"~",xvar)),
              fun.aggregate = function(x) sum(is.na(x)))
  dl <- melt(dl, id.vars=newvar, variable.name=xvar, value.name=newval)
  ggplot(dl, aes_string(x=xvar, y=newvar)) + 
    geom_tile(aes_string(fill=newval), color="white") +
    geom_text(aes_string(label=newval)) + 
    scale_fill_continuous("Missing (N)", low="gray", high="cornflowerblue") +
    labs(title="Missing Data Pattern")
}

Test data:

df <- iris
set.seed(4)
df[sample(nrow(df), 20), 2] <- NA
df[sample(nrow(df), 30), 3] <- NA
df[sample(nrow(df), 15), 4] <- NA

ggplot_missing2(df)

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