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Generates a volcano plot using ggplot2 This function generates a base volcano plot highlighting genes associated with a certain GOterm that can then be expanded upon using further ggplot functions.

Source: R/plot_de_summaries.R
go_volcano.Rd

Generates a volcano plot using ggplot2 This function generates a base volcano plot highlighting genes associated with a certain GOterm that can then be expanded upon using further ggplot functions.

Usage

go_volcano(
  res_de,
  res_enrich,
  mapping = "org.Hs.eg.db",
  term_index,
  logfc_cutoff = 1,
  FDR = 0.05,
  col_to_use = NULL,
  enrich_col = "genes",
  gene_col_separator = ",",
  down_col = "black",
  up_col = "black",
  highlight_col = "tomato",
  n_overlaps = 20
)

Arguments

res_de

An object containing the results of the Differential Expression analysis workflow (e.g. DESeq2, edgeR or limma). Currently, this can be a DESeqResults object created using the DESeq2 framework.

res_enrich

A enrichment result object created by for example using run_topGO()

mapping

Which org.XX.eg.db package to use for annotation - select according to the species

term_index

The location (row) of your GO term of interest in your enrichment result

logfc_cutoff

A numeric value that sets the cutoff for the xintercept argument of ggplot

FDR

The pvalue threshold to us for counting genes as de and therefore also where to draw the line in the plot. Default is 0.05

col_to_use

The column in your differential expression results containing your gene symbols. If you don't have one it is created automatically

enrich_col

column name from your res_enrich where the genes associated with your GOterm are stored (for example see the run_topGO() result in mosdef)

gene_col_separator

The separator used to split the genes. If you used topGO or goseq this is a "," which is the default. (For an example see the run_topGO() result in mosdef) If you used clusterProfiler this has to be set to "/". (For example see the run_cluPro() result in mosdef)

down_col

The colour for your downregulated genes, default is "gray"

up_col

The colour for your upregulated genes, default is "gray"

highlight_col

The colour for the genes associated with your GOterm default is "tomato"

n_overlaps

Number of overlaps ggrepel is supposed to allow when labeling (for more info check ggrepel documentation)

Value

A ggplot2 volcano plot object that can be extended upon by the user

Examples


library("org.Hs.eg.db")

data(res_de_macrophage, package = "mosdef")
data(res_enrich_macrophage_topGO, package = "mosdef")

p <- go_volcano(
  res_macrophage_IFNg_vs_naive,
  res_enrich = res_enrich_macrophage_topGO,
  term_index = 1,
  logfc_cutoff = 1,
  mapping = "org.Hs.eg.db",
  n_overlaps = 20
)
#> 'select()' returned 1:many mapping between keys and columns
#> Warning: Direct call of 'as.data.frame.numeric()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.numeric()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.numeric()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.numeric()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.numeric()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead
#> Warning: Direct call of 'as.data.frame.numeric()' is deprecated.  Use 'as.data.frame.vector()' or 'as.data.frame()' instead

p
#> Warning: Removed 17706 rows containing missing values or values outside the scale range
#> (`geom_label_repel()`).
#> Warning: ggrepel: 70 unlabeled data points (too many overlaps). Consider increasing max.overlaps