gs_alluvial: Alluvial (sankey) plot for a set of genesets and the...

Description Usage Arguments Value Examples

View source: R/gs_alluvial.R

Description

Generate an interactive alluvial plot linking genesets to their associated genes

Usage

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gs_alluvial(res_enrich, res_de, annotation_obj, n_gs = 5, gs_ids = NULL)

gs_sankey(res_enrich, res_de, annotation_obj, n_gs = 5, gs_ids = NULL)

Arguments

res_enrich

A data.frame object, storing the result of the functional enrichment analysis. See more in the main function, GeneTonic(), to check the formatting requirements (a minimal set of columns should be present).

res_de

A DESeqResults object.

annotation_obj

A data.frame object with the feature annotation information, with at least two columns, gene_id and gene_name.

n_gs

Integer value, corresponding to the maximal number of gene sets to be displayed

gs_ids

Character vector, containing a subset of gs_id as they are available in res_enrich. Lists the gene sets to be displayed.

Value

A plotly object

Examples

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library("macrophage")
library("DESeq2")
library("org.Hs.eg.db")
library("AnnotationDbi")

# dds object
data("gse", package = "macrophage")
dds_macrophage <- DESeqDataSet(gse, design = ~line + condition)
rownames(dds_macrophage) <- substr(rownames(dds_macrophage), 1, 15)
dds_macrophage <- estimateSizeFactors(dds_macrophage)

# annotation object
anno_df <- data.frame(
  gene_id = rownames(dds_macrophage),
  gene_name = mapIds(org.Hs.eg.db,
                     keys = rownames(dds_macrophage),
                     column = "SYMBOL",
                     keytype = "ENSEMBL"),
  stringsAsFactors = FALSE,
  row.names = rownames(dds_macrophage)
)

# res object
data(res_de_macrophage, package = "GeneTonic")
res_de <- res_macrophage_IFNg_vs_naive

# res_enrich object
data(res_enrich_macrophage, package = "GeneTonic")
res_enrich <- shake_topGOtableResult(topgoDE_macrophage_IFNg_vs_naive)
res_enrich <- get_aggrscores(res_enrich, res_de, anno_df)

gs_alluvial(res_enrich = res_enrich,
            res_de = res_de,
            annotation_obj = anno_df,
            n_gs = 4)
# or using the alias...
gs_sankey(res_enrich = res_enrich,
          res_de = res_de,
          annotation_obj = anno_df,
          n_gs = 4)

GeneTonic documentation built on Nov. 8, 2020, 5:27 p.m.