plot_pathways {func2vis}

Plot clean enriched pathways as a bubble plot

Description

Make a bubble plot of clean enriched pathways obtained from 'ConsensusPathDB' by performing gene set overexpression analysis. Colours represent the clusters to which each pathway belongs. You need to run the function clean_pathways to obtain the input data frame.

Usage

plot_pathways(final_df_pathway, total_no_background_genes, fontsize)

Arguments

final_df_pathway

Clean and clustered pathways obtained using clean_pathways.

total_no_background_genes

Total no of genes in the background set.

fontsize

Font size of the pathways to be displayed on y-axis.

Value

Returns a bubble plot of type ggplot. Colours represent the clusters to which each pathway belongs.

Note

[e-mail]

Author(s)

Raghvendra Mall

See Also

See Also as clean_pathways, plot_pathways_stacked_barplot, plot_go_terms

Examples

data("t.tests.treatment.sign")
data("enriched_pathways")
revised_pathway <- clean_pathways(df_case_vs_ctrl=t.tests.treatment.sign,
                                  df_pathway = enriched_pathways)
p <- plot_pathways(revised_pathway)
p