plot_down: Plot top 'n' most significantly enriched pathways in the...
In mirvie/mirmisc: Non-Modeling Helper Functions For Mirvie R Coders

Description Usage Arguments Value See Also Examples

Plot top n most significantly enriched pathways in the upward or downward direction.

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plot_down(fgsea_out, padj_thresh = 0.05, n = 20)

plot_up(fgsea_out, padj_thresh = 0.05, n = 20)

`fgsea_out`	Output of `fgsea::fgsea()` or `fgsea_basic()`.
`padj_thresh`	Adjusted p-value threshold.
`size_thresh`	number of genes to show.

A ggplot2::ggplot().

Other Arkady: check_sample_descs(), collapse_tech_reps(), deseq_contrasts(), deseq_pairs(), deseq_wide(), fgsea_basic(), plot_cond_paired_pearson(), plot_metrics_global(), plot_var_mean_ratio(), prep_gsea_input_gene_set(), prep_gsea_input_lfc(), prep_rd_input(), reconcile_names()

rs_genes <- arrow::read_feather(
  system.file("extdata", "rs_genes_draw_3_4.feather", package = "mirmisc")
)
rs_meta <- arrow::read_feather(
  system.file("extdata", "rs_meta_draw_3_4.feather", package = "mirmisc")
)
ddsx <- deseq_wide(rs_genes, rs_meta, compvar = "meta_draw")
dsq_contrasts <- deseq_contrasts(ddsx, compr = c("4", "3"))
prepped_gsea_input_lfc <- prep_gsea_input_lfc(dsq_contrasts)
prepped_gsea_input_gene_set <- prep_gsea_input_gene_set("C8")
fgs <- fgsea_basic(prepped_gsea_input_lfc, prepped_gsea_input_gene_set)
plot_down(fgs)
plot_up(fgs)