get_gene_expression_box_plot: Generate a box plot

In cparsania/parcutils: Utility Functions To Deal Day To Day Bioinformatics Tasks.

Generate a box plot

Description

Generate a box plot

Usage

get_gene_expression_box_plot(
  x,
  samples = NULL,
  genes = NULL,
  group_replicates = FALSE,
  convert_log2 = TRUE
)

Arguments

x	an abject of class "parcutils". This is an output of the function run_deseq_analysis().
samples	a character vector denoting samples to plot in boxplot, default NULL. If set to NULL all samples are accounted.
genes	a character vector denoting genes to consider for boxplot, default NULL. If set to NULL all genes are accounted.
group_replicates	logical, default FALSE, whether to group replicates in individual plots.
convert_log2	logical, default TRUE, whether to plot log2(noralised expression + 1) or not.

Value

an object of class ggplot2

Examples

count_file <- system.file("extdata","toy_counts.txt" , package = "parcutils")
count_data <- readr::read_delim(count_file, delim = "\t")

sample_info <- count_data %>% colnames() %>% .[-1]  %>%
 tibble::tibble(samples = . , groups = rep(c("control" ,"treatment1" , "treatment2"), each = 3) )


res <- run_deseq_analysis(counts = count_data ,
                         sample_info = sample_info,
                         column_geneid = "gene_id" ,
                         group_numerator = c("treatment1", "treatment2") ,
                         group_denominator = c("control"))

get_gene_expression_box_plot(x = res ) %>% print()

get_gene_expression_box_plot(x = res , group_replicates = TRUE ) %>% print()

cparsania/parcutils documentation built on Oct. 27, 2024, 4:55 a.m.