| Title: | Interactive Volcano Plot |
| Version: | 0.0.1 |
| Description: | Generate interactive volcano plots for exploring gene expression data. Built with 'ggplot2', the plots are rendered interactive using 'ggiraph', enabling users to hover over points to display detailed information or click to trigger custom actions. |
| Depends: | R (≥ 4.1.0) |
| Imports: | dplyr, ggplot2, ggiraph, ggrepel, rlang |
| Suggests: | quarto, yulab.utils |
| VignetteBuilder: | quarto |
| License: | GPL (≥ 3) |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.3.2 |
| NeedsCompilation: | no |
| Packaged: | 2025-09-09 06:56:20 UTC; HUAWEI |
| Author: | Guangchuang Yu 
[aut, cre, cph] |
| Maintainer: | Guangchuang Yu <guangchuangyu@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2025-09-11 09:20:07 UTC |
ivolcano
Description
interactive volcano plot
Usage
ivolcano(
data,
logFC_col = "logFC",
pval_col = "adj.P.Val",
gene_col = "gene",
title = "Volcano Plot",
interactive = TRUE,
onclick_fun = NULL,
pval_cutoff = 0.05,
logFC_cutoff = 1,
top_n = 10,
label_mode = "separate",
fontface = "italic",
label_sig_only = TRUE,
threshold_line = list(color = "black", linetype = "dashed", linewidth = 0.5),
sig_colors = c(Up = "red", Down = "blue", Not_Significant = "grey70"),
size_by = "none"
)
Arguments
data |
A data frame that contains minimal information with gene id, logFC and adjusted P values |
logFC_col |
column name in 'data' that stored the logFC values |
pval_col |
column name in 'data' that stored the adjusted P values |
gene_col |
column name in 'data' that stored the gene IDs |
title |
plot title |
interactive |
whether plot the graph in interactive mode |
onclick_fun |
effects when click on the dot (gene), default is NULL |
pval_cutoff |
cutoff of the adjusted P values |
logFC_cutoff |
cutoff of the logFC values |
top_n |
top N genes to display the labels (gene ID) |
label_mode |
one of 'all' or 'separate' (default). If label_mode = 'all', top_n genes with minimal p values will be displayed, otherwise, top_n up-regulated and top_n down-regulated genes will be displayed. |
fontface |
one of 'plain', 'bold', 'italic' (default) and their combination, e.g. 'bold.italic' |
label_sig_only |
whether filter significant genes before subset 'top_n' genes |
threshold_line |
customize threshold line style (e.g., line color, type, and width) |
sig_colors |
customize colors for up- and down-regulated, and non-significant genes |
size_by |
one of "none" (default), "negLogP", or "absLogFC" to scale dot sizes. |
Value
volcano plot
Author(s)
Guangchuang Yu
Examples
# example data
f <- system.file('extdata/airway.rds', package='ivolcano')
df <- readRDS(f)
# plot
ivolcano(df,
logFC_col = "log2FoldChange",
pval_col = "padj",
gene_col = "symbol",
top_n = 5,
onclick_fun=onclick_genecards)
onclick_fanyi
Description
generate onclick function from fanyi::gene_summary() output
Usage
onclick_fanyi(gene_summary, cols)
Arguments
gene_summary |
output from |
cols |
selected columns from 'gene_summary' |
Value
onclick function
Author(s)
Guangchuang Yu
onclick_genecards
Description
onclick function to popup genecards webpage
Usage
onclick_genecards(gene)
Arguments
gene |
query gene |
Value
onclick action
Author(s)
Guangchuang Yu