get_pairwise_corr_plot: Get a scatter plot showing correlation between replicates.

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

Get a scatter plot showing correlation between replicates.

Description

Get a scatter plot showing correlation between replicates.

Usage

get_pairwise_corr_plot(x, samples = NULL, genes = NULL)

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 scatter plot, default NULL. If set to NULL all samples are accounted.
genes	a character vector denoting genes to consider in scatter plot, default NULL. If set to NULL all genes are accounted.#'

Value

a named list.

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"))

cp <- get_pairwise_corr_plot(res)


names(cp) %>% print()

cp[1] %>% print

cp[2] %>% print

cp[3] %>% print

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