create_filtered_plot: create_filtered_plot

In w-korani/keggseq: KEGG analysis and visualizing of differentially expressed genes

Description

create_filtered_plot generates a scatter plot of the output of the calculate_kegg function with passing a specific filter

Usage

create_filtered_plot(dataset,filter_name,filter_value)

Arguments

dataset	The output dataset of the calculate_kegg function
filter_name	a string of one of the following filters can be used: background_gene_numbers, all genes included in the pathways. deg_gene_numbers, the differentially expressed genes included int the pathway. pvalue, the p-values. adjusted_pvalue, the adjusted p-values. qvalue, the q-values.
filter_value	A string starts by <,>,==,<= or >= then the values for filtering

Value

returns a plot.

Examples

a <- list_species("arachis")
b <- grep_datasets(c("adu","aip"))
deg_list <- as.matrix(b[b$kegg_pathways=='00061',1])[,1]
c <- calculate_kegg(b,deg_list)
create_filtered_plot(c,"deg_gene_numbers",">0")

w-korani/keggseq documentation built on May 3, 2019, 7:10 p.m.