volcano_plot {promor} | R Documentation |
Volcano plot
Description
This function generates volcano plots to visualize differentially expressed proteins between groups.
Usage
volcano_plot(
fit_df,
adj_method = "BH",
sig = "adjP",
cutoff = 0.05,
lfc = 1,
line_fc = TRUE,
line_p = TRUE,
palette = "viridis",
text_size = 10,
label_top = FALSE,
n_top = 10,
save = FALSE,
file_path = NULL,
file_name = "Volcano_plot",
file_type = "pdf",
plot_height = 7,
plot_width = 7,
dpi = 80
)
Arguments
fit_df |
A |
adj_method |
Method used for adjusting the p-values for multiple
testing. Default is |
sig |
Criteria to denote significance. Choices are |
cutoff |
Cutoff value for p-values and adjusted p-values. Default is 0.05. |
lfc |
Minimum absolute log2-fold change to use as threshold for differential expression. |
line_fc |
Logical. If |
line_p |
Logical. If |
palette |
Viridis color palette option for plots. Default is
|
text_size |
Text size for axis text, labels etc. |
label_top |
Logical. If |
n_top |
The number of top hits to label with protein name when
|
save |
Logical. If |
file_path |
A string containing the directory path to save the file. |
file_name |
File name to save the plot. Default is "Volcano_plot." |
file_type |
File type to save the plot. Default is |
plot_height |
Height of the plot. Default is 7. |
plot_width |
Width of the plot. Default is 7. |
dpi |
Plot resolution. Default is |
Details
Volcano plots show log-2-fold change on the x-axis, and based on the significance criteria chosen, either -log10(p-value) or -log10(adjusted p-value) on the y-axis.
-
volcano_plot
requires afit_df
object from performing differential expression analysis withfind_dep.
User has the option to choose criteria that denote significance.
Value
A ggplot2
plot object.
Author(s)
Chathurani Ranathunge
See Also
Examples
## Create a volcano plot with default settings.
volcano_plot(ecoli_fit_df)
## Change significance criteria and cutoff
volcano_plot(ecoli_fit_df, cutoff = 0.1, sig = "P")
## Label top 30 differentially expressed proteins and
## change the color palette of the plot
volcano_plot(ecoli_fit_df, label_top = TRUE, n_top = 30, palette = "mako")