Create a volcano plot from a data.frame containing differential expression results.
Usage
plot_volcano(
df,
x = "logFC",
y = "FDR",
lab = NULL,
fdr = 0.05,
lfc = 0,
label_sig = FALSE,
annotate_counts = TRUE,
up_color = "red2",
down_color = "royalblue2",
nonde_color = "grey40",
up_alpha = 1,
down_alpha = 1,
nonde_alpha = 1,
up_size = 1,
down_size = 1,
nonde_size = 1,
up_shape = 16,
down_shape = 16,
nonde_shape = ".",
xmin_label_offset = 0.8,
xmax_label_offset = 0.8,
ymax_label_offset = 0.9,
lab_size = 6,
lab_digits = 1,
x_axis_limits = NULL,
y_axis_limits = NULL,
...
)Arguments
- df
dataframe containing columns with gene names, p-values, and log-fold changes.
- x
logFC column. Default (logFC)
- y
FDR or p-value column. Default (FDR)
- lab
column containing gene id or labels. Default (NULL)
- fdr
significance level cutoff for plotting. Values below the given fdr threshold are considered significant. Default (0.05)
- lfc
log-fold-change cutoff for plotting. Values greater than the abs(lfc) and less than fdr are displayed as differentially expressed. Default (0)
- label_sig
TRUE/FALSE. apply ggrepel::geom_text_labels to significant DE genes.
- annotate_counts
TRUE/FALSE. Annotate the plot with the summarized gene counts
- up_color
Point color of the up-regulated features
- down_color
Point color of the down-regulated features
- nonde_color
Point color of the unperturbed features
- up_alpha
Point alpha of the up-regulated features
- down_alpha
Point alpha of the down-regulated features
- nonde_alpha
Point alpha of the unperturbed features
- up_size
Point size of the up-regulated features
- down_size
Point size of the down-regulated features
- nonde_size
Point size of the unperturbed features
- up_shape
Point shape of the up-regulated features
- down_shape
Point shape of the down-regulated features
- nonde_shape
Point shape of the unperturbed features
- xmin_label_offset
numeric. Value between 0 and 1 inclusive to control the x-position of the count annotation label for the 'down' counts
- xmax_label_offset
numeric. Value between 0 and 1 inclusive to control the x-position of the count annotation label for the 'up' counts
- ymax_label_offset
numeric. Value between 0 and 1 inclusive to control the y-position of the count labels.
- lab_size
numeric. Size of the label if annotate_counts = TRUE. Default 6.
- lab_digits
numeric. The number of digits used when rounding percentage values when annotate_counts=TRUE. Default (1)
- x_axis_limits
numeric vector of axis limits supplied to ggplot2::coord_cartesian(). Default (NULL)
- y_axis_limits
numeric vector of axis limits supplied to ggplot2::coord_cartesian(). Default (NULL)
- ...
Additional arguments passed to
ggrepel::geom_text_repel
Examples
plot_volcano(GSE161650_de, fdr = 0.01, lfc = log2(2))
