Create barplot for Boolean values

[SimonG]

Dear community,
I would like to create a barplot from this data frame :
df = data.frame(geneA = c(0,1,0,1,1,1,1,0,1,0), geneB = c(0,1,1,1,1,0,0,1,1,0), geneC = c(0,1,1,1,0,0,1,1,0,1) ,cluster = c(1,3,1,2,1,3,2,3,2,1))

Each gene is expressed (1) or not (0), and I would like to visualize for each cluster a barplot of the expression ratio for each of the 3 genes, I can't find the way to visualize that...

Best regards

Simon

[jms]

Hi Simon!

If I understand you correctly, you can do the plot like this:

library(tidyverse)

mydf <- data.frame(geneA = c(0,1,0,1,1,1,1,0,1,0), geneB = c(0,1,1,1,1,0,0,1,1,0), geneC = c(0,1,1,1,0,0,1,1,0,1) ,cluster = c(1,3,1,2,1,3,2,3,2,1))
#Convert data
mydf_long<-mydf%>%pivot_longer(starts_with("gene"),names_to="Gene",values_to="Expression")
#Count occurrences per cluster
mydf_count<-mydf_long%>%group_by(cluster,Gene,Expression)%>%tally()
  

mydf_count%>%
  ggplot(aes(x=Gene,y = n,fill=factor(Expression)))+
  geom_bar(stat = "identity",position = "dodge")+
  facet_wrap(~cluster)+
  scale_fill_discrete(name = "Expression", labels = c("Silent", "Expressed"))

^{Created on 2021-01-12 by the reprex package (v0.3.0)}

Explanation:

At first, I convert your data into the long format, so that every observation has its own row. Then I count how many times each gene expressed / silent in each cluster and create the bar chart per cluster.

Is that the kind of visualisation you were thinking of?

[SimonG]

@jms

library(tidyverse)

mydf <- data.frame(geneA = c(0,1,0,1,1,1,1,0,1,0), geneB = c(0,1,1,1,1,0,0,1,1,0), geneC = c(0,1,1,1,0,0,1,1,0,1) ,cluster = c(1,3,1,2,1,3,2,3,2,1))
#Convert data
mydf_long<-mydf%>%pivot_longer(starts_with("gene"),names_to="Gene",values_to="Expression")
#Count occurrences per cluster
mydf_count<-mydf_long%>%group_by(cluster,Gene,Expression)%>%tally()
  

mydf_count%>%
  ggplot(aes(x=Gene,y = n,fill=factor(Expression)))+
  geom_bar(stat = "identity",position = "dodge")+
  facet_wrap(~cluster)+
  scale_fill_discrete(name = "Expression", labels = c("Silent", "Expressed"))

Hello,
Thank you for your answer
Yes this is the kind of representation I would like, but expressed as a ratio of expressed/silent for each gene (0-100%) , instead having 2 bars for the count of each category
Thanks again

[FJCC]

Will this work for you?

library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
library(ggplot2)
library(tidyr)
df = data.frame(geneA = c(0,1,0,1,1,1,1,0,1,0), 
                geneB = c(0,1,1,1,1,0,0,1,1,0), 
                geneC = c(0,1,1,1,0,0,1,1,0,1) ,
                cluster = c(1,3,1,2,1,3,2,3,2,1))
LongDF <- df %>% pivot_longer(geneA:geneC,, names_to = "Gene", values_to = "Value")
head(LongDF)
#> # A tibble: 6 x 3
#>   cluster Gene  Value
#>     <dbl> <chr> <dbl>
#> 1       1 geneA     0
#> 2       1 geneB     0
#> 3       1 geneC     0
#> 4       3 geneA     1
#> 5       3 geneB     1
#> 6       3 geneC     1
SummaryDF <- LongDF %>% group_by(cluster, Gene) %>% 
  summarize(Fraction_Expressed = mean(Value))
#> `summarise()` regrouping output by 'cluster' (override with `.groups` argument)
head(SummaryDF)
#> # A tibble: 6 x 3
#> # Groups:   cluster [2]
#>   cluster Gene  Fraction_Expressed
#>     <dbl> <chr>              <dbl>
#> 1       1 geneA              0.25 
#> 2       1 geneB              0.5  
#> 3       1 geneC              0.5  
#> 4       2 geneA              1    
#> 5       2 geneB              0.667
#> 6       2 geneC              0.667
ggplot(SummaryDF, aes(x = cluster, y = Fraction_Expressed, fill = Gene)) + geom_col(position = "dodge")

^{Created on 2021-01-12 by the reprex package (v0.3.0)}

[SimonG]

That's perfect, thanks to both of you !