Making a Stacked BAR chart in ggplot from Excel file

Question

[Ap1438]

Cl  S1  S2  S3
A   39  42  40
B   15  20  18
C   15  4   10
D   4   5   5

I have a excel sheet with clade names A,B,C and D of 3 samples S1,S2 and S3 having relative abundance values shown above.

I want to make a Stacked Bar chart and used this code.

library("readxl")    
library(dplyr)    
library(ggplot2)    
library(scales)    
read_excel("relative_abundance(1).xlsx",sheet = "Only_P")     
ggplot(data, aes(fill=CL, lable=y, x='S1')) +     
    geom_bar(position="dodge", stat="identity")

But I didn't succeed. I am new to R and don't know much can anyone please help me.

I want to make a stacked bar chart as the image I have attached.

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. If your code has long lines with a single command, break those lines into multiple lines with proper escape sequences so they're easier to read and still run when copy-pasted. I've done it for you this time.

[Ap1438]

Thank you for helping.I will keep in mind your valuable suggestions.

Answer 1

[bioinformatics2020]

Your data is not in the correct format to be able to create the stacked barplot you have posted above. Here's a quick example of how you can get your data into that format (by "pivotting" the data from a wide-format, to a long format.) Assuming we have a data frame as such:

dt <- data.frame(CL = LETTERS[1:4],
               S1 = c(39, 15, 15, 4),
               S2 = c(42,20,4,5),
               S3 = c(40, 18, 10, 5))

head(dt)

CL S1 S2 S3
1  A 39 42 40
2  B 15 20 18
3  C 15  4 10
4  D  4  5  5

dt <- pivot_longer(dt, cols = -CL, names_to = "Samples", values_to = "Expression")

ggplot(dt, aes(x = Samples, y = Expression, fill = CL)) +
  geom_bar(stat = "identity")][1]

[Ap1438]

It worked .Thank you for your valuable time and suggestion.