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!
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deathmagnetic20 •
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"))
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:
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"))
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?
What's challenging about it?
Yes with my low code level, sorry!
I meant I dont know how to include all the barcodes and cell types but manually.
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.
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Can you repost the image? It's not showing up.
Reposted the image, sorry!