How to reorder the place of stacked barplot based on their y value in ggplot?

Question

I'm trying to reorder the stacked bar plot in decreasing order, I mean the bar of Esophageal placed first, but my script doesn't work.

Here is the df

                           Cancer.Study Alteration.Frequency     Alteration.Type Alteration.Count
1                  Esophageal Carcinoma            10.2702703       Amplification               19
2                  Esophageal Carcinoma             1.0810811      Point mutation                2
3        Liver Hepatocellular Carcinoma             0.2652520 Multiple alteration                1
4        Liver Hepatocellular Carcinoma             5.8355438       Amplification               22
5        Liver Hepatocellular Carcinoma             0.7957560      Point mutation                3
6                Stomach Adenocarcinoma             6.4853556       Amplification               31
7          Bladder Urothelial Carcinoma             2.9197080       Amplification               12
8                   Lung Adenocarcinoma             2.7131783       Amplification               14
9          Lung Squamous Cell Carcinoma             2.5948104       Amplification               13
10 Uterine Corpus Endometrial Carcinoma             0.9174312       Amplification                5

And here is my script

ggplot(df,
       aes(fill=factor(Alteration.Type, 
                       levels = c('Point mutation','Amplification','Deep deletion', 'Multiple alteration')),
           x=reorder(Cancer.Study, -Alteration.Frequency)), y=Alteration.Frequency)) + 
  geom_bar(position="stack", stat="identity")+theme_bw()

Thanks for any help

Answer 1

You could use reorder for your fill aesthetic like this:

df <- read.table(text = "                           Cancer.Study Alteration.Frequency     Alteration.Type Alteration.Count
1                  Esophageal.Carcinoma            10.2702703       Amplification               19
2                  Esophageal.Carcinoma             1.0810811      Point.mutation                2
3        Liver.Hepatocellular.Carcinoma             0.2652520 Multiple.alteration                1
4        Liver.Hepatocellular.Carcinoma             5.8355438       Amplification               22
5        Liver.Hepatocellular.Carcinoma             0.7957560      Point.mutation                3
6                Stomach.Adenocarcinoma             6.4853556       Amplification               31
7          Bladder.Urothelial.Carcinoma             2.9197080       Amplification               12
8                   Lung.Adenocarcinoma             2.7131783       Amplification               14
9          Lung.Squamous.Cell.Carcinoma             2.5948104       Amplification               13
10 Uterine.Corpus.Endometrial.Carcinoma             0.9174312       Amplification                5", header = TRUE)

library(ggplot2)
ggplot(df, aes(fill=reorder(Alteration.Type, -Alteration.Frequency),
           x=Cancer.Study, y=Alteration.Frequency)) + 
  geom_bar(position="stack", stat="identity") + 
  labs(fill = "Alteration.Type") +
  theme_bw() +
  theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1)) 

^{Created on 2022-09-10 with reprex v2.0.2}

Please note : I added some dots to your whitespaces in your data.

Answer 2

By default, reorder uses the respective mean. You however want to order by the absolute count. That's why you have to specify FUN = sum in the reoder() function.

See below with the df table of Quinten

library(tidyverse)
    
ggplot(df, aes(x = reorder(Cancer.Study, -Alteration.Frequency, FUN = sum),
       y = Alteration.Frequency,
       fill = Alteration.Type)) + 
       geom_bar(position="stack", stat="identity") + 
       labs(fill = "Alteration.Type") +
       ylab("Alteration Frequency") +
       xlab("Cancer Study") +
       theme_bw() +
       theme(axis.text.x = element_text(angle = 45, hjust=1))