stacked Bar plot displaying values

[saurabh]

my dataframe

tata4 <- data.frame(Subtype = c("Prostate", "Oesophagus", "Lung"),  
alive = c(88, 22, 100), dead = c(12, 55, 17), uncertain = c(10, 2, 2), total = c(186,46,202)) 

what I want is this - A stacked barplot for each of the 'prostate', 'oesophagus and Lung. The columns should be subdivided vertically into the number alive,dead and uncertain according to each cancer. (with each bar displaying the total).

I'm struggling to find the right codes. I can't seem to find a way of making the 'fill' function the values of each tumour site.

Can someone please help.

[andresrcs]

What have you tried so far? what is your specific problem?, we are more inclined towards helping you with specific coding problems rather than doing your work for you.

Could you please turn this into a self-contained REPRoducible EXample (reprex)? A reprex makes it much easier for others to understand your issue and figure out how to help.

If you've never heard of a reprex before, you might want to start by reading this FAQ:

FAQ: How to do a minimal reproducible example ( reprex ) for beginners

A minimal reproducible example consists of the following items: A minimal dataset, necessary to reproduce the issue The minimal runnable code necessary to reproduce the issue, which can be run on the given dataset, and including the necessary information on the used packages. Let's quickly go over each one of these with examples: Minimal Dataset (Sample Data) You need to provide a data frame that is small enough to be (reasonably) pasted on a post, but big enough to reproduce your issue. Let's say, as an example, that you are working with the iris data frame head(iris) #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> 1 5.1 3.5 1.4 0.…

[saurabh]

No worries, I had a bash. Here is my dataframe

tata3 <- data.frame( stringsAsFactors = TRUE, Subtype = c("lung", "prostate", "oesophagus"),  
alive = c(88, 22, 100), dead = c(12, 55, 17), uncertain = c(10, 2, 2), total = c(186,46,202))

Then remove the 'Total' column using subset function, as this is superfluous.

tata3 <- subset(tata3, select= -c(total))

The convert data into long from wide by this code

tata3_long <- tata3

tata3_long$Subtype <- as.factor(1:nrow(tata3_long))

tata3_long <- melt(tata3_long, id.vars = "Subtype")

Then the following code to get the plot

ggplot(tata3_long, aes(x = Subtype, y = value, fill = variable)) + geom_bar(stat = "identity")

The only problem I am now left with is how to make the Subtype appear on the X Axis (i.e. Lung, Prostate, Oesophagus) rather than the numbers (1,2,3,). I think it is something to do with the

as.factor(1:nrow(tata3_long)

But I cannot modify this line of code successfully. Plot attached.

Cheers.

[saurabh]

Think I might actually have worked in out.

data_long1 <- melt(tata3,id.vars = c("Subtype"))

better way of changing data to long from wide
and then the following code

ggplot(data_long1, aes(x = Subtype, y = value, fill = variable)) + geom_bar(stat = "identity")  

I renamed the lung to HPC

[andresrcs]

The reshape2::melt() function and more generally the reshape2 package has long been superseded by the tidyr package, the modern equivalent would be the tidyr::pivot_longer() function, consider this alternative solution:

# Library calls
library(tidyverse)

# Sample data in a copy/paste friendly format
tata3 <- data.frame(
    stringsAsFactors = TRUE,
    Subtype = c("lung", "prostate", "oesophagus"),
    alive = c(88, 22, 100),
    dead = c(12, 55, 17),
    uncertain = c(10, 2, 2),
    total = c(186, 46, 202))

# Relevant code
tata3 %>% 
    select(-total) %>% 
    pivot_longer(cols = -Subtype,
                 names_to = "variable",
                 values_to = "value") %>%
    mutate(Subtype = str_replace(Subtype, "lung", "HPC")) %>% 
    ggplot(aes(x = Subtype, y = value, fill = variable)) +
    geom_col()

^{Created on 2022-03-02 by the reprex package (v2.0.1)}

Also, please be aware that your "reprex" is missing library calls, it is an important part of a reproducible example so next time please try to make a proper self-contained reproducible example and ideally run the code before posting so you can make sure it is functional.