R: How can I order a character column by another column (factor or character label) in ggplots

Question

I'm trying to plot Alluvial Plots using ggplot. So far it went well until I want to try to clean the plot up.

As you can see on the plot, from left to right, the first stratum/column is the ID column then it follows by a column of labels: disease risk. What I want to achieve is in the out plot, instead of having the patient IDs zigzagging, I want them to be ordered by disease risk column, so that all the high risk IDs are all together on top, followed by low risk then the not filled ones. In this way it is much easier to see if there's any relations.

I have looked around for the arrange() and order() functions, they seem to do the trick for my actual input data but once I pass that data frame in ggplot, the output figure is still scrambled.

I thought of set the IDs to factor, then use levels=.... But this is not very smart if the patient ID keeps growing.

Is there a smarter way? please enlighten me. I have attached a link towards the sample data.

https://drive.google.com/file/d/16Pd8V3MCgEHmZEButVi2UjDiwZWklK-T/view?usp=sharing

My code to plot the graph :

library(tidyr)
library(ggplot2)
library(ggalluvial)
library(RColorBrewer)

# Define the number of colors you want
nb.cols <- 10
mycolor1 <- colorRampPalette(brewer.pal(8, "Set2"))(nb.cols)
mycolors <- c("Black")

 
#read the data
CLL3S.plusrec <- read.csv("xxxx.CSV", as.is = T)
CLL3S.plusrec$risk_by_DS <- factor(CLL3S.plusrec$risk_by_DS, levels = c("low_risk", "high_risk", "Not filled"))
CLL3S.plusrec$`Enriched response phenotype` <- factor(CLL3S.plusrec$`Enriched response phenotype`, levels = c("Live cells","Pre-dead", "TN & PDB", "PDB & Lenalidomide", "TN & STSVEN & Live cells","Mixed"))

#here I reorder the dataframe and it looks good 
#but the output ggplot changes the order of ID in the output graph
OR <- with(CLL3S.plusrec, CLL3S.plusrec[order(risk_by_DS),])


d <-ggplot(OR, aes(y = count, 
          axis1= Patient.ID,
          axis2= risk_by_DS,
          axis3 = `Cluster assigned consensus`, 
          axis4 = `Cluster assigned single drug`,
          axis5 = `Enriched response phenotype`
          
      )) +
  scale_x_discrete(limits = c("Patient ID","Disease Risk", "Consensus cluster", "Single-drug cluster", "Enriched drug response by Phenoptype")) +
  geom_alluvium(aes(fill=`Cluster assigned consensus`)) +
  geom_stratum(width = 1/3, fill = c(mycolor1[1:69],mycolor1[1:3],mycolor1[1:8],mycolor1[1:8],mycolor1[1:6]), color = "red") +
  #geom_stratum() +
  geom_text(stat = "stratum", aes(label = after_stat(stratum)), size=3) +
  theme(axis.title.x = element_text(size = 15,  face="bold"))+
  theme(axis.title.y = element_text(size = 15,  face="bold"))+
  theme(axis.text.x = element_text(size = 10,  face="bold")) +
  theme(axis.text.y = element_text(size = 10,  face="bold")) +
  labs(fill = "Consensus clusters")+
  guides(fill=guide_legend(override.aes = list(color=mycolors)))+
  ggtitle("Patient flow between the Consensus clusters and Single-drug treated clusters",
      "3S stimulated patients")
  print(d)

Duck · Accepted Answer · 2020-10-23T16:39:34.907

Not sure if this is what you want, try formating the risk column in this way:

library(tidyr)
library(ggplot2)
library(ggalluvial)
library(RColorBrewer)

# Define the number of colors you want
nb.cols <- 10
mycolor1 <- colorRampPalette(brewer.pal(8, "Set2"))(nb.cols)
mycolors <- c("Black")


#read the data
CLL3S.plusrec <- read.csv("test data.CSV", as.is = T)
CLL3S.plusrec$risk_by_DS <- factor(CLL3S.plusrec$risk_by_DS,
                                   levels = c("high_risk","low_risk","Not filled"),ordered = T)
CLL3S.plusrec$Enriched.response.phenotype <- factor(CLL3S.plusrec$Enriched.response.phenotype, levels = c("Live cells","Pre-dead", "TN & PDB", "PDB & Lenalidomide", "TN & STSVEN & Live cells","Mixed"))

#here I reorder the dataframe and it looks good 
#but the output ggplot changes the order of ID in the output graph
OR <- with(CLL3S.plusrec, CLL3S.plusrec[order(risk_by_DS),])


ggplot(OR, aes(y = count, 
                   axis1= reorder(Patient.ID,risk_by_DS),
                   axis2= risk_by_DS,
                   axis3 = reorder(Cluster.assigned.consensus,risk_by_DS), 
                   axis4 = reorder(Cluster.assigned.single.drug,risk_by_DS),
                   axis5 = reorder(Enriched.response.phenotype,risk_by_DS)
                   
)) +
  scale_x_discrete(limits = c("Patient ID","Disease Risk", "Consensus cluster", "Single-drug cluster", "Enriched drug response by Phenoptype")) +
  geom_alluvium(aes(fill=Cluster.assigned.consensus)) +
  geom_stratum(width = 1/3, fill = c(mycolor1[1:69],mycolor1[1:3],mycolor1[1:8],mycolor1[1:8],mycolor1[1:6]), color = "red") +
  #geom_stratum() +
  geom_text(stat = "stratum", aes(label = after_stat(stratum)), size=3) +
  theme(axis.title.x = element_text(size = 15,  face="bold"))+
  theme(axis.title.y = element_text(size = 15,  face="bold"))+
  theme(axis.text.x = element_text(size = 10,  face="bold")) +
  theme(axis.text.y = element_text(size = 10,  face="bold")) +
  labs(fill = "Consensus clusters")+
  guides(fill=guide_legend(override.aes = list(color=mycolors)))+
  ggtitle("Patient flow between the Consensus clusters and Single-drug treated clusters",
          "3S stimulated patients")

Output:

Also in my read.csv() the quotes got off and dots are in the variables. That is why your original quoted variables now have dots. Maybe an issue from reading.

Update:

#Update
OR <- with(CLL3S.plusrec, CLL3S.plusrec[order(risk_by_DS),])
OR <- OR[order(OR$risk_by_DS,OR$Patient.ID),]
OR$Patient.ID <- factor(OR$Patient.ID,levels = unique(OR$Patient.ID),ordered = T)
#Plot
ggplot(OR, aes(y = count, 
                   axis1= reorder(Patient.ID,risk_by_DS),
                   axis2= risk_by_DS,
                   axis3 = reorder(Cluster.assigned.consensus,risk_by_DS), 
                   axis4 = reorder(Cluster.assigned.single.drug,risk_by_DS),
                   axis5 = reorder(Enriched.response.phenotype,risk_by_DS)
                   
)) +
  scale_x_discrete(limits = c("Patient ID","Disease Risk", "Consensus cluster", "Single-drug cluster", "Enriched drug response by Phenoptype")) +
  geom_alluvium(aes(fill=Cluster.assigned.consensus)) +
  geom_stratum(width = 1/3, fill = c(mycolor1[1:69],mycolor1[1:3],mycolor1[1:8],mycolor1[1:8],mycolor1[1:6]), color = "red") +
  #geom_stratum() +
  geom_text(stat = "stratum", aes(label = after_stat(stratum)), size=3) +
  theme(axis.title.x = element_text(size = 15,  face="bold"))+
  theme(axis.title.y = element_text(size = 15,  face="bold"))+
  theme(axis.text.x = element_text(size = 10,  face="bold")) +
  theme(axis.text.y = element_text(size = 10,  face="bold")) +
  labs(fill = "Consensus clusters")+
  guides(fill=guide_legend(override.aes = list(color=mycolors)))+
  ggtitle("Patient flow between the Consensus clusters and Single-drug treated clusters",
          "3S stimulated patients")

Output:

Thank you for getting back to me. First thank you for pointing out why my variables now have dots, I was annoyed by that too. For the output figure, I think we are on the track. However, I wanted the Patient IDs essentially grouped according high /low/not filled, so i should see no messy crossings of the flow between patient ID to disease risk stratum, but 3 thick non-crossing horizontal streams. — ML33M, Oct 23 '20 at 16:27
@ML33M I see now, arranging can be the way to solve. Let me check if that works! — Duck, Oct 23 '20 at 16:28
@ML33M I have added an update. Please test if that works for you! — Duck, Oct 23 '20 at 16:39
this worked beautifully. Could you just make some simple explanations of the principles of OR <- with(CLL3S.plusrec, CLL3S.plusrec[order(risk_by_DS),]) OR <- OR[order(OR$risk_by_DS,OR$Patient.ID),]. Why my first line on its own wont work but we have to put in the second line like you did? — ML33M, Oct 23 '20 at 17:24
@ML33M Sure, a pleasure. Maybe the nature of `with` is not changing the data. When you use the second line you are modifying directly the variable to be ordered. In that way you can get the groups in the order you want. Sometimes, I prefer do the changes directly to the dataframe instead of using with. I hope that was clear enough for you! — Duck, Oct 23 '20 at 17:28
fantastic. Thank you. I love the feeling of learning something new! — ML33M, Oct 23 '20 at 17:55

R: How can I order a character column by another column (factor or character label) in ggplots

1 Answers1