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MA-plot from base means and log fold changes

Source: R/plot_de_summaries.R
plot_ma.Rd

MA-plot from base means and log fold changes, in the ggplot2 framework, with additional support to annotate genes if provided.

Usage

plot_ma(
  res_de,
  FDR = 0.05,
  point_alpha = 0.2,
  sig_color = "red",
  annotation_obj = NULL,
  draw_y0 = TRUE,
  hlines = NULL,
  title = NULL,
  xlab = "mean of normalized counts - log10 scale",
  ylim = NULL,
  add_rug = TRUE,
  intgenes = NULL,
  intgenes_color = "steelblue",
  labels_intgenes = TRUE,
  labels_repel = TRUE
)

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.

FDR

Numeric value, the significance level for thresholding adjusted p-values

point_alpha

Alpha transparency value for the points (0 = transparent, 1 = opaque)

sig_color

Color to use to mark differentially expressed genes. Defaults to red

annotation_obj

A data.frame object, with row.names as gene identifiers (e.g. ENSEMBL ids) and a column, gene_name, containing e.g. HGNC-based gene symbols. Optional

draw_y0

Logical, whether to draw the horizontal line at y=0. Defaults to TRUE.

hlines

The y coordinate (in absolute value) where to draw horizontal lines, optional

title

A title for the plot, optional

xlab

X axis label, defaults to "mean of normalized counts - log10 scale"

ylim

Vector of two numeric values, Y axis limits to restrict the view

add_rug

Logical, whether to add rug plots in the margins

intgenes

Vector of genes of interest. Gene symbols if a symbol column is provided in res_de, or else the identifiers specified in the row names

intgenes_color

The color to use to mark the genes on the main plot.

labels_intgenes

Logical, whether to add the gene identifiers/names close to the marked plots

labels_repel

Logical, whether to use ggrepel::geom_text_repel for placing the labels on the features to mark

Value

An object created by ggplot

Details

The genes of interest are to be provided as gene symbols if a symbol column is provided in res_de, or else by using the identifiers specified in the row names

Examples

data(res_de_macrophage, package = "mosdef")

plot_ma(res_macrophage_IFNg_vs_naive, FDR = 0.05, hlines = 1)


plot_ma(res_macrophage_IFNg_vs_naive,
  FDR = 0.1,
  intgenes = c(
    "ENSG00000103196", # CRISPLD2
    "ENSG00000120129", # DUSP1
    "ENSG00000163884", # KLF15
    "ENSG00000179094" # PER1
  )
)
#> 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