How to reproduce a stacked bar chart in R

Question

[deathmagnetic20]

Hi,

I have used the analytical tool CIBERSORTx to impute gene expression profiles and provide an estimation of the abundances of member cell types in a mixed cell population, using RNAseq and TCGA data. The output table have TCGA barcodes in rows, and cell types in columns. I would like to generate a stacked bar chart using R, like this one:

Any idea?

Thanks!

[bioinformatics2020]

Can you repost the image? It's not showing up.

[deathmagnetic20]

Reposted the image, sorry!

Answer 1

[bioinformatics2020]

Data is a data.frame that has the TCGA barcodes in a column called "barcodes", relative percentage in a column called "percent", and cell types in "cell_types."

if(!require("tidyverse")) install.packages("tidyverse")
library(ggplot2)
ggplot(data, mapping = aes(x = barcodes, y = percent, fill =  cell_types)) + 
    geom_bar(position= "stack", stat = "identity")

EDIT: In case you want to change the colors of the cell_types, you can add scale_fill_manual with labels being the names of the cell-types, and values being the color hex code you want:

 ggplot(data, mapping = aes(x = barcodes, y = percent, fill =  cell_types)) + 
        geom_bar(position= "stack", stat = "identity") +
        scale_fill_manual(labels = c("cell_type1", "cell_type2", "cell_type3"), values = c("#000000", "#000000", "#000000"))

[deathmagnetic20]

Thank you!

My problem is that I have a table data format like this one, so I dont know how to reorder in order to have the columns you said:

[bioinformatics2020]

library(ggplot2)
set.seed(1)
test_df <- data.frame(mixture = c("TCGA.P7.ASNX", "TCGA.P7.A5NY", "TCGA.P8.A5KD",
                       "TCGA.P7.ASNN", "TCGA.P7.A5NB", "TCGA.P8.A5KE"),
           cell_type_a = runif(6),
           cell_type_b = runif(6),
           cell_type_c = runif(6))

#mixture cell_type_a cell_type_b cell_type_c
#1 TCGA.P7.ASNX   0.2655087  0.94467527   0.6870228
#2 TCGA.P7.A5NY   0.3721239  0.66079779   0.3841037
#3 TCGA.P8.A5KD   0.5728534  0.62911404   0.7698414
#4 TCGA.P7.ASNN   0.9082078  0.06178627   0.4976992
#5 TCGA.P7.A5NB   0.2016819  0.20597457   0.7176185
#6 TCGA.P8.A5KE   0.8983897  0.17655675   0.9919061


 test_df <- test_df %>% pivot_longer(!mixture, names_to = "cell_types", values_to = "percent") %>%
      rename(barcodes = mixture)

#barcodes     cell_types  percent
 #  <chr>        <chr>         <dbl>
 #1 TCGA.P7.ASNX cell_type_a  0.266 
 #2 TCGA.P7.ASNX cell_type_b  0.945 
 #3 TCGA.P7.ASNX cell_type_c  0.687 
 #4 TCGA.P7.A5NY cell_type_a  0.372 
 #5 TCGA.P7.A5NY cell_type_b  0.661 
 #6 TCGA.P7.A5NY cell_type_c  0.384 
 #7 TCGA.P8.A5KD cell_type_a  0.573 
 #8 TCGA.P8.A5KD cell_type_b  0.629 
 #9 TCGA.P8.A5KD cell_type_c  0.770 
#10 TCGA.P7.ASNN cell_type_a  0.908 
#11 TCGA.P7.ASNN cell_type_b  0.0618
#12 TCGA.P7.ASNN cell_type_c  0.498 
#13 TCGA.P7.A5NB cell_type_a  0.202 
#14 TCGA.P7.A5NB cell_type_b  0.206 
#15 TCGA.P7.A5NB cell_type_c  0.718 
#16 TCGA.P8.A5KE cell_type_a  0.898 
#17 TCGA.P8.A5KE cell_type_b  0.177 
#18 TCGA.P8.A5KE cell_type_c  0.992 

ggplot(data = test_df, mapping = aes(x = barcodes, y = percent, fill = cell_types )) + 
  geom_bar(position = "stack", stat = "identity") + 
  scale_fill_manual(labels = c("cell_type_a", "cell_type_b", "cell_type_c"), values = c("#000000",
                                                                                        "#000000",
                                                                                        "#000000"))

[deathmagnetic20]

I will try it, thanks!

Challenging, cause I have to include 178 rows (barcodes) and 28 (cell types). Is there a simple code to do it?

[bioinformatics2020]

What's challenging about it?

[deathmagnetic20]

Yes with my low code level, sorry!

I meant I dont know how to include all the barcodes and cell types but manually.

[bioinformatics2020]

Ah, you don't have to! That portion of the code when I type the cell_types and colors (scale_fill_manual) is optional! You can simply use the code above to transform your data.frame into the correct format, and then use ggplot without the scale_fill_manual:

ggplot(data = test_df, mapping = aes(x = barcodes, y = percent, fill = cell_types )) + 
  geom_bar(position = "stack", stat = "identity")

It'll automatically add colors.