#Relative abundance bar plot#
I’ve generated a ggplot graph using data from three tables: OTU table, OTU_taxonomy, and metadata. Despite the graph’s overall quality, I’m encountering vertical white spaces within the lines. How can I eliminate these lines from the plot? Any insights would be valuable. Below is my code, and I’ve attached the graph for reference.
library(ggplot2)
library(tidyverse)
Tab <- read_tsv("otu_table_sat.tsv")
Tab <- read_tsv("otu_table_sat.tsv",
col_types = cols(otu_id = col_character(),
.default = col_number()))
dat <- Tab %>%
pivot_longer(-otu_id, names_to = "sample_id", values_to = "count")
dat
Tax <- read_tsv("otu_taxonomy_sat.tsv",
col_types = cols(.default = "character"))
Tax
dat <- dat %>%
left_join(Tax, by = "otu_id")
dat
Meta <- read_tsv("sample_metadata_sat.tsv",
col_types = cols(.default = col_character()))
Meta
dat <- dat %>%
left_join(Meta, by = "sample_id")
dat
#this is the final code for generating bar graph:
dat %>%
ggplot(aes(x = sample_id, y = count)) +
facet_grid(~ Group, scales = "free_x", space = "free_x") +
geom_bar(aes(fill = Phylum), stat = "identity", position = "fill") +
scale_y_continuous(name = "Relative abundance",
labels = scales::percent) +
theme(axis.text.x = element_text(angle = 90, size = 10, face = "bold"),
axis.text.y = element_text(color = "black"),
strip.text = element_text(face = "bold"),
strip.background = element_blank())
Please you can provide the answer if anything I am missing here in my code and any sugession.
Relative abundance bar plot: https://i.sstatic.net/4IECt.png
It could be easier if you provide a reproducible example, but my guess on what’s happening is the following:
- Those white lines are probably the result of grouping in the original dataset.
- You have NA’s or NULL values or something in those variables.
Solution 1: Add the color parameter to the geom_bar() function
geom_bar(aes(fill = Phylum, color = Phylum), stat = "identity", position = "fill")
Solution 2: Get rid of the NA’s in your dataset.
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