Combine 4 bar-plots into one graph in R - r

Question

I want to create a bar-plot using R, which will describe V gene frequency in 4 compartments in the body.
I have this table:
head(my_data)
# A tibble: 6 x 8
Tumor ...2 BM ...4 DLN ...6 Blood ...8
<chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
1 V hit frequency V hit frequency V hit frequency V hit frequency
2 IGHV3-1~ 0.54386205~ IGHV10-~ 0.22723742~ IGHV1-5~ 0.1132060~ IGHV5-~ 0.1417894~
3 IGHV5-1~ 0.16148068~ IGHV5-6~ 7.62620114~ IGHV5-1~ 0.1010986~ IGHV7-~ 0.1133675~
4 IGHV10-~ 3.18440869~ IGHV1-6~ 5.68199208~ IGHV1-6~ 8.1465889~ IGHV2-~ 6.4763474~
5 IGHV5-6~ 2.71468704~ IGHV3-1~ 5.24995831~ IGHV5-6~ 7.1625980~ IGHV5-~ 6.3008918~
6 IGHV6-3~ 2.71460485~ IGHV1-9~ 4.19517008~ IGHV1-7~ 4.7428361~ IGHV1-~ 5.0785188~
>
dput(my_data)
structure(list(Tumor = c("V hit", "IGHV3-1*00", "IGHV5-17*00",
"IGHV10-1*00", "IGHV5-6*00", "IGHV6-3*00", "IGHV2-9*00", "IGHV5-4*00",
"IGHV1-9*00"), ...2 = c("frequency", "0.54386205717535796", "0.161480687577157",
"3.1844086931792998E-2", "2.7146870412713998E-2", "2.7146048502561901E-2",
"2.4098405658687001E-2", "2.1746920713615302E-2", "1.6909157558532301E-2"
), BM = c("V hit", "IGHV10-3*00", "IGHV5-6*00", "IGHV1-62-3*00",
"IGHV3-1*00", "IGHV1-9*00", "IGHV10-1*00", "IGHV2-9*00", "IGHV4-2*00"
), ...4 = c("frequency", "0.22723742785161699", "7.62620114066965E-2",
"5.6819920833780603E-2", "5.2499583155365397E-2", "4.1951700840313098E-2",
"3.5214806321420301E-2", "3.2695465872415799E-2", "3.0610100659414E-2"
), DLN = c("V hit", "IGHV1-50*00", "IGHV5-17*00", "IGHV1-62-3*00",
"IGHV5-6*00", "IGHV1-7*00", "IGHV1-4*00", "IGHV6-3*00", "IGHV10-1*00"
), ...6 = c("frequency", "0.113206013467841", "0.101098647226429",
"8.1465889741680994E-2", "7.1625980782229995E-2", "4.7428361184553902E-2",
"4.4690299561054497E-2", "4.3051740808241597E-2", "3.9509373582839201E-2"
), Blood = c("V hit", "IGHV5-6*00", "IGHV7-3*00", "IGHV2-9*00",
"IGHV5-17*00", "IGHV1-67*00", "IGHV1-62-3*00", "IGHV1-7*00",
"IGHV1-9*00"), ...8 = c("frequency", "0.141789453276464", "0.113367584335014",
"6.4763474214811906E-2", "6.3008918185343196E-2", "5.0785188057386597E-2",
"5.0504071345482703E-2", "4.52113222179139E-2", "3.8183404420318E-2"
)), row.names = c(NA, -9L), class = c("tbl_df", "tbl", "data.frame"
))
(^this is just a little part of my entire data.)
Tumor,blood,BM, and DLN are my compartments, and each of them has its V genes and thier frequencies.
I want 1 bar-plot: X-axis will be V genes and for each v gene, I want 4 bars, 1 for each compartment.
Y-axis will be the frequencies.
I'm assuming I need to create df that has only one column of all v genes and multiple columns of frequencies in each of the compartments, but I don't know how to do that.
Any help will be appreciated !!
Thanks, Ligal.

Answer 1

Clean up data
df <- df[-1,] # remove unwanted row
compart <- names(df)[seq(1,8,2)] # compartment names
not_compart <- names(df)[seq(2,8,2)] # not compartment names
# melt data from wide to long
library('data.table')
setDT(df)[, id := 1:.N] # assign id
df <- melt(df, id.vars = 'id',
measure.vars = list(compart, not_compart ),
variable.name = "compartments",
value.name = c("genes", "frequency"))
# change names of compartments
df[, compartments := factor(compartments, levels = seq_along(compart), labels = compart)]
# change frequency values from character to numeric
df[, frequency := as.numeric(frequency)]
Data - output
head(df)
# id compartments genes frequency
# 1: 1 Tumor IGHV3-1*00 0.54386206
# 2: 2 Tumor IGHV5-17*00 0.16148069
# 3: 3 Tumor IGHV10-1*00 0.03184409
# 4: 4 Tumor IGHV5-6*00 0.02714687
# 5: 5 Tumor IGHV6-3*00 0.02714605
# 6: 6 Tumor IGHV2-9*00 0.02409841
Plot
library('ggplot2')
ggplot(data = df, mapping = aes(x = genes, y = frequency)) +
geom_bar(stat = "identity") +
coord_flip() +
facet_wrap(. ~ compartments, scales = "free_y" ) +
theme_bw()
Graph
Plot2
ggplot(data = df, mapping = aes(x = compartments, y = frequency)) +
geom_bar(stat = "identity") +
coord_flip() +
facet_wrap(. ~ genes, scales = "free_y" ) +
theme_bw()
Graph2
Plot-3
ggplot(data = df, mapping = aes(x = genes, y = frequency, color = compartments, fill = compartments, group = compartments)) +
geom_bar(stat = "identity", position = position_dodge(width = 0.9)) +
theme_bw() +
theme(axis.text.x = element_text(angle = 45, hjust = 1))
Graph-3

Answer 2

Try this:
library(dplyr)
library(tidyr)
library(purrr)
library(ggplot2)
my_data <- structure(list(Tumor = c(
"V hit", "IGHV3-1*00", "IGHV5-17*00",
"IGHV10-1*00", "IGHV5-6*00", "IGHV6-3*00", "IGHV2-9*00", "IGHV5-4*00",
"IGHV1-9*00"
), ...2 = c(
"frequency", "0.54386205717535796", "0.161480687577157",
"3.1844086931792998E-2", "2.7146870412713998E-2", "2.7146048502561901E-2",
"2.4098405658687001E-2", "2.1746920713615302E-2", "1.6909157558532301E-2"
), BM = c(
"V hit", "IGHV10-3*00", "IGHV5-6*00", "IGHV1-62-3*00",
"IGHV3-1*00", "IGHV1-9*00", "IGHV10-1*00", "IGHV2-9*00", "IGHV4-2*00"
), ...4 = c(
"frequency", "0.22723742785161699", "7.62620114066965E-2",
"5.6819920833780603E-2", "5.2499583155365397E-2", "4.1951700840313098E-2",
"3.5214806321420301E-2", "3.2695465872415799E-2", "3.0610100659414E-2"
), DLN = c(
"V hit", "IGHV1-50*00", "IGHV5-17*00", "IGHV1-62-3*00",
"IGHV5-6*00", "IGHV1-7*00", "IGHV1-4*00", "IGHV6-3*00", "IGHV10-1*00"
), ...6 = c(
"frequency", "0.113206013467841", "0.101098647226429",
"8.1465889741680994E-2", "7.1625980782229995E-2", "4.7428361184553902E-2",
"4.4690299561054497E-2", "4.3051740808241597E-2", "3.9509373582839201E-2"
), Blood = c(
"V hit", "IGHV5-6*00", "IGHV7-3*00", "IGHV2-9*00",
"IGHV5-17*00", "IGHV1-67*00", "IGHV1-62-3*00", "IGHV1-7*00",
"IGHV1-9*00"
), ...8 = c(
"frequency", "0.141789453276464", "0.113367584335014",
"6.4763474214811906E-2", "6.3008918185343196E-2", "5.0785188057386597E-2",
"5.0504071345482703E-2", "4.52113222179139E-2", "3.8183404420318E-2"
)), row.names = c(NA, -9L), class = c("tbl_df", "tbl", "data.frame"))
# Tidy the dataset
my_data <- slice(my_data, -1)
## Separate the data columns for each compartment and put them in a list
df_tidy <- list(tumor = my_data[1:2], bm = my_data[3:4], dln = my_data[5:6], blood = my_data[7:8]) %>%
## Rename the data columns
map(~ rename(.x, v_hit = 1, freq = 2)) %>%
## Bind the four dfs together into one df
bind_rows(.id = "compartment") %>%
## Convert the frequencies to numeric values
mutate(freq = as.numeric(freq))
head(df_tidy)
#> # A tibble: 6 x 3
#> compartment v_hit freq
#> <chr> <chr> <dbl>
#> 1 tumor IGHV3-1*00 0.544
#> 2 tumor IGHV5-17*00 0.161
#> 3 tumor IGHV10-1*00 0.0318
#> 4 tumor IGHV5-6*00 0.0271
#> 5 tumor IGHV6-3*00 0.0271
#> 6 tumor IGHV2-9*00 0.0241
# Barplot
ggplot(df_tidy, aes(v_hit, freq, fill = compartment)) +
geom_col() +
coord_flip() +
facet_wrap(~compartment, scales = "free_y") +
guides(fill = FALSE)
Created on 2020-03-29 by the reprex package (v0.3.0)