EnhancedVolcano: Volcano plots represent a useful way to visualise the results...

Description Usage Arguments Details Value Author(s) Examples

View source: R/EnhancedVolcano.R

Description

Volcano plots represent a useful way to visualise the results of differential expression analyses. Here, we present a highly-configurable function that produces publication-ready volcano plots [@EnhancedVolcano]. EnhancedVolcano will attempt to fit as many variable names in the plot window as possible, thus avoiding 'clogging' up the plot with labels that could not otherwise have been read.

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
EnhancedVolcano(
  toptable,
  lab,
  x,
  y,
  selectLab = NULL,
  xlim = c(min(toptable[[x]], na.rm = TRUE) - 1.5, max(toptable[[x]], na.rm = TRUE) +
    1.5),
  ylim = c(0, max(-log10(toptable[[y]]), na.rm = TRUE) + 5),
  xlab = bquote(~Log[2] ~ "fold change"),
  ylab = bquote(~-Log[10] ~ italic(P)),
  axisLabSize = 18,
  title = "Volcano plot",
  subtitle = bquote(italic(EnhancedVolcano)),
  caption = paste0("total = ", nrow(toptable), " variables"),
  titleLabSize = 18,
  subtitleLabSize = 14,
  captionLabSize = 14,
  pCutoff = 1e-05,
  FCcutoff = 1,
  cutoffLineType = "longdash",
  cutoffLineCol = "black",
  cutoffLineWidth = 0.4,
  pointSize = 2,
  labSize = 5,
  labCol = "black",
  labFace = "plain",
  labhjust = 0.5,
  labvjust = 1.5,
  boxedLabels = FALSE,
  shape = 19,
  shapeCustom = NULL,
  col = c("grey30", "forestgreen", "royalblue", "red2"),
  colCustom = NULL,
  colAlpha = 1/2,
  colGradient = NULL,
  colGradientBreaks = c(pCutoff, 1),
  colGradientLabels = c("0", "1.0"),
  colGradientLimits = c(0, 1),
  legendLabels = c("NS", expression(Log[2] ~ FC), "p-value", expression(p - value ~ and
    ~ log[2] ~ FC)),
  legendPosition = "top",
  legendLabSize = 14,
  legendIconSize = 5,
  legendDropLevels = TRUE,
  encircle = NULL,
  encircleCol = "black",
  encircleFill = "pink",
  encircleAlpha = 3/4,
  encircleSize = 2.5,
  shade = NULL,
  shadeFill = "grey",
  shadeAlpha = 1/2,
  shadeSize = 0.01,
  shadeBins = 2,
  drawConnectors = FALSE,
  widthConnectors = 0.5,
  typeConnectors = "closed",
  endsConnectors = "first",
  lengthConnectors = unit(0.01, "npc"),
  colConnectors = "grey10",
  arrowheads = TRUE,
  hline = NULL,
  hlineType = "longdash",
  hlineCol = "black",
  hlineWidth = 0.4,
  vline = NULL,
  vlineType = "longdash",
  vlineCol = "black",
  vlineWidth = 0.4,
  gridlines.major = TRUE,
  gridlines.minor = TRUE,
  border = "partial",
  borderWidth = 0.8,
  borderColour = "black",
  raster = FALSE
)

Arguments

toptable

A data-frame of test statistics (if not, a data frame, an attempt will be made to convert it to one). Requires at least the following: column for variable names (can be rownames); a column for log2 fold changes; a column for nominal or adjusted p-value.

lab

A column name in toptable containing variable names. Can be rownames(toptable).

x

A column name in toptable containing log2 fold changes.

y

A column name in toptable containing nominal or adjusted p-values.

selectLab

A vector containing a subset of lab.

xlim

Limits of the x-axis.

ylim

Limits of the y-axis.

xlab

Label for x-axis.

ylab

Label for y-axis.

axisLabSize

Size of x- and y-axis labels.

title

Plot title.

subtitle

Plot subtitle.

caption

Plot caption.

titleLabSize

Size of plot title.

subtitleLabSize

Size of plot subtitle.

captionLabSize

Size of plot caption.

pCutoff

Cut-off for statistical significance. A horizontal line will be drawn at -log10(pCutoff).

FCcutoff

Cut-off for absolute log2 fold-change. Vertical lines will be drawn at the negative and positive values of log2FCcutoff.

cutoffLineType

Line type for FCcutoff and pCutoff ('blank', 'solid', 'dashed', 'dotted', 'dotdash', 'longdash', 'twodash').

cutoffLineCol

Line colour for FCcutoff and pCutoff.

cutoffLineWidth

Line width for FCcutoff and pCutoff.

pointSize

Size of plotted points for each variable. Can be a single value or a vector of sizes.

labSize

Size of labels for each variable.

labCol

Colour of labels for each variable.

labFace

Font face of labels for each variable.

labhjust

Horizontal adjustment of label for each variable.

labvjust

Vertical adjustment of label for each variable.

boxedLabels

Logical, indicating whether or not to draw labels in boxes.

shape

Shape of the plotted points. Either a single value for all points, or 4 values corresponding to the default 4 legend labels specified by legendLabels.

shapeCustom

Named vector / key-value pairs that will over-ride the default shape scheme. The order must match that of toptable. Names / keys relate to groups / categories; values relate to shape encodings.

col

Colour shading for plotted points, corresponding to the default 4 legend labels specified by legendLabels.

colCustom

Named vector / key-value pairs that will over-ride the default colour scheme. The order must match that of toptable. Names / keys relate to groups / categories; values relate to colour.

colAlpha

Alpha for purposes of controlling colour transparency of variable points.

colGradient

If activated, over-rides the default discrete colour scheme and replaces it with a continous scheme that shades based on nominal or adjusted p-value specified by y. For example, c('red2', 'blue2').

colGradientBreaks

Break-points for the two colours specified by colGradient.

colGradientLabels

Labels for the break-points specified by colGradientBreaks.

colGradientLimits

Limits of the colour scheme specified by colGradient, i.e., max and min possible p-values.

legendLabels

Plot legend text labels.

legendPosition

Position of legend ('top', 'bottom', 'left', 'right').

legendLabSize

Size of plot legend text.

legendIconSize

Size of plot legend icons / symbols.

legendDropLevels

Logical, drop unused factor levels from legend.

encircle

A vector of variable names to encircle.

encircleCol

Colour of the encircled line.

encircleFill

Colour fill of the encircled region.

encircleAlpha

Alpha for purposes of controlling colour transparency of encircled region.

encircleSize

Line width of the encircled line.

shade

A vector of variable names to shade.

shadeFill

Colour of shaded regions.

shadeAlpha

Alpha for purposes of controlling colour transparency of shaded region.

shadeSize

Size of the shade contour lines.

shadeBins

Number of bins for the density of the shade.

drawConnectors

Logical, indicating whether or not to connect plot labels to their corresponding points by line connectors.

widthConnectors

Line width of connectors.

typeConnectors

Have the arrow head open ('open') or filled ('closed')?

endsConnectors

Which end of connectors to draw arrow head? ('last', 'first', 'both').

lengthConnectors

Length of the connectors.

colConnectors

Line colour of connectors.

arrowheads

Logical, indicating whether or not to draw arrow heads or or just have straight lines.

hline

Draw one or more horizontal lines passing through this/these values on y-axis. For single values, only a single numerical value is necessary. For multiple lines, pass these as a vector, e.g., c(60,90).

hlineType

Line type for hline ('blank', 'solid', 'dashed', 'dotted', 'dotdash', 'longdash', 'twodash').

hlineCol

Colour of hline.

hlineWidth

Width of hline.

vline

Draw one or more vertical lines passing through this/these values on x-axis. For single values, only a single numerical value is necessary. For multiple lines, pass these as a vector, e.g., c(60,90).

vlineType

Line type for vline ('blank', 'solid', 'dashed', 'dotted', 'dotdash', 'longdash', 'twodash').

vlineCol

Colour of vline.

vlineWidth

Width of vline.

gridlines.major

Logical, indicating whether or not to draw major gridlines.

gridlines.minor

Logical, indicating whether or not to draw minor gridlines.

border

Add a border for just the x and y axes ('partial') or the entire plot grid ('full')?

borderWidth

Width of the border on the x and y axes.

borderColour

Colour of the border on the x and y axes.

raster

Logical, indicating whether to rasterize the geom_point layer.

Details

Volcano plots represent a useful way to visualise the results of differential expression analyses. Here, we present a highly-configurable function that produces publication-ready volcano plots [@EnhancedVolcano]. EnhancedVolcano will attempt to fit as many variable names in the plot window as possible, thus avoiding 'clogging' up the plot with labels that could not otherwise have been read.

Value

A ggplot2 object.

Author(s)

Kevin Blighe <kevin@clinicalbioinformatics.co.uk>

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
library('pasilla')
pasCts <- system.file('extdata', 'pasilla_gene_counts.tsv',
  package='pasilla', mustWork=TRUE)
pasAnno <- system.file('extdata', 'pasilla_sample_annotation.csv',
  package='pasilla', mustWork=TRUE)
cts <- as.matrix(read.csv(pasCts,sep='\t',row.names='gene_id'))
coldata <- read.csv(pasAnno, row.names=1)
coldata <- coldata[,c('condition','type')]
rownames(coldata) <- sub('fb', '', rownames(coldata))
cts <- cts[, rownames(coldata)]
library('DESeq2')
dds <- DESeqDataSetFromMatrix(countData = cts,
  colData = coldata,
  design = ~ condition)

featureData <- data.frame(gene=rownames(cts))
mcols(dds) <- DataFrame(mcols(dds), featureData)
dds <- DESeq(dds)
res <- results(dds)

EnhancedVolcano(res,
  lab = rownames(res),
  x = 'log2FoldChange',
  y = 'pvalue',
  pCutoff = 10e-4,
  FCcutoff = 1.333,
  xlim = c(-5.5, 5.5),
  ylim = c(0, -log10(10e-12)),
  pointSize = 1.5,
  labSize = 2.5,
  title = 'DESeq2 results',
  subtitle = 'Differential expression',
  caption = 'FC cutoff, 1.333; p-value cutoff, 10e-4',
  legendPosition = "right",
  legendLabSize = 14,
  col = c('grey30', 'forestgreen', 'royalblue', 'red2'),
  colAlpha = 0.9,
  drawConnectors = TRUE,
  hline = c(10e-8),
  widthConnectors = 0.5)

EnhancedVolcano documentation built on Nov. 8, 2020, 8:29 p.m.