| Title: | Fast Visualization For Glycoverse |
|---|---|
| Description: | Provides a unified interface for visualizing glycomics data within the 'glycoverse' ecosystem. Implements 'autoplot()' methods for various data structures including statistical results from 'glystats', experimental data from 'glyexp', and glycan structures from 'glyrepr'. Designed for rapid data exploration and quality assessment rather than publication-quality figure generation. |
| Authors: | Bin Fu [aut, cre] (ORCID: <https://orcid.org/0000-0001-8567-2997>) |
| Maintainer: | Bin Fu <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 0.6.0 |
| Built: | 2026-05-31 09:49:11 UTC |
| Source: | https://github.com/glycoverse/glyvis |
Visualization for glyexp::experiment() (glyexp_experiment object).
Possible types of plots:
"heatmap": (Default) Expression heatmap with columns as samples and rows as variables.
"boxplot": Boxplot of expression values for each sample.
## S3 method for class 'glyexp_experiment' autoplot(object, type = "heatmap", group_col = "group", ...)## S3 method for class 'glyexp_experiment' autoplot(object, type = "heatmap", group_col = "group", ...)
object |
A |
type |
The type of plot, one of "heatmap" (default) or "boxplot". |
group_col |
A character string specifying where to find the group information. It should be a column in the sample information tibble. Defaults to "group". Only applicable to "boxplot". |
... |
Ignored. |
A ggplot object.
Visualization for glystats_anova_res and glystats_kruskal_res.
Draw a dotchart for p-values.
## S3 method for class 'glystats_anova_res' autoplot(object, p_cutoff = 0.05, p_col = "p_adj", ...) ## S3 method for class 'glystats_kruskal_res' autoplot(object, p_cutoff = 0.05, p_col = "p_adj", ...)## S3 method for class 'glystats_anova_res' autoplot(object, p_cutoff = 0.05, p_col = "p_adj", ...) ## S3 method for class 'glystats_kruskal_res' autoplot(object, p_cutoff = 0.05, p_col = "p_adj", ...)
object |
A |
p_cutoff |
The p-value cutoff. Defaults to 0.05. |
p_col |
The column name for p-value. Defaults to "p_adj". Can also be "p_val" (raw p-values without multiple testing correction). |
... |
Other arguments passed to underlying functions. |
A ggplot object.
Visualization for glystats::gly_cor() results (glystats_cor_res objects).
## S3 method for class 'glystats_cor_res' autoplot(object, ...)## S3 method for class 'glystats_cor_res' autoplot(object, ...)
object |
A |
... |
Other arguments passed to |
A ggplot object.
Visualization for results from glystats::gly_cox() (glystats_cox_res objects).
Draw a dotchart for p-values.
## S3 method for class 'glystats_cox_res' autoplot(object, p_cutoff = 0.05, p_col = "p_adj", ...)## S3 method for class 'glystats_cox_res' autoplot(object, p_cutoff = 0.05, p_col = "p_adj", ...)
object |
A |
p_cutoff |
The p-value cutoff. Defaults to 0.05. |
p_col |
The column name for p-value. Defaults to "p_adj". Can also be "p_val" (raw p-values without multiple testing correction). |
... |
Ignored. |
A ggplot object.
Visualization for results from glystats::gly_enrich_go(), glystats::gly_enrich_kegg(), and glystats::gly_enrich_reactome()
(glystats_go_ora_res, glystats_kegg_ora_res, and glystats_reactome_ora_res objects).
Possible types of plots:
"dotplot" (default): Dotplot showing p-value, gene counts, and gene ratios.
"barplot": Barplot showing p-values and gene counts.
"network": Network plot showing terms and their relationships.
## S3 method for class 'glystats_go_ora_res' autoplot(object, type = "dotplot", ...) ## S3 method for class 'glystats_kegg_ora_res' autoplot(object, type = "dotplot", ...) ## S3 method for class 'glystats_reactome_ora_res' autoplot(object, type = "dotplot", ...)## S3 method for class 'glystats_go_ora_res' autoplot(object, type = "dotplot", ...) ## S3 method for class 'glystats_kegg_ora_res' autoplot(object, type = "dotplot", ...) ## S3 method for class 'glystats_reactome_ora_res' autoplot(object, type = "dotplot", ...)
object |
A |
type |
The type of plot, one of "dotplot" (default), "barplot", or "network". |
... |
Other arguments passed to underlying functions
( |
A ggplot object.
enrichplot::dotplot(), enrichplot::barplot.enrichResult(), enrichplot::emapplot()
Visualization for results from glystats::gly_hclust() (glystats_hclust_res object).
Draw a dendrogram.
## S3 method for class 'glystats_hclust_res' autoplot(object, ...)## S3 method for class 'glystats_hclust_res' autoplot(object, ...)
object |
A |
... |
Additional arguments passed to |
A ggplot object.
Visualization for results from glystats::gly_limma() (glystats_limma_res objects).
Only 2-group comparison is supported, and a volcano plot is drawn.
## S3 method for class 'glystats_limma_res' autoplot( object, contrast = NULL, log2fc_cutoff = 1, p_cutoff = 0.05, p_col = "p_adj", ... )## S3 method for class 'glystats_limma_res' autoplot( object, contrast = NULL, log2fc_cutoff = 1, p_cutoff = 0.05, p_col = "p_adj", ... )
object |
A |
contrast |
A character string specifying the contrast to plot, in the format of "group1_vs_group2". Must be one of the contrasts in the result. When there is only one contrast (two-group comparison), it can be NULL (default). |
log2fc_cutoff |
The log2 fold change cutoff. Defaults to 1. |
p_cutoff |
The p-value cutoff. Defaults to 0.05. |
p_col |
The column name for p-value. Defaults to "p_adj". Can also be "p_val" (raw p-values without multiple testing correction). |
... |
Other arguments passed to underlying functions. |
A ggplot object.
Visualization for results from glystats::gly_oplsda() (glystats_oplsda_res object).
Possible types of plots:
"scores" (default): Plot scores for samples.
"loadings": Plot loadings for variables.
"vip": Plot VIP scores for variables.
"variance": Plot explained variance for each component.
"s-plot": Plot the correlation between p1 and pcorr1.
## S3 method for class 'glystats_oplsda_res' autoplot( object, type = "scores", y_type = "o1", groups = NULL, group_col = NULL, ... )## S3 method for class 'glystats_oplsda_res' autoplot( object, type = "scores", y_type = "o1", groups = NULL, group_col = NULL, ... )
object |
A |
type |
The type of plot, one of "loadings", "scores", "vip", "variance", or "s-plot". Defaults to "scores". |
y_type |
What to plot on the y-axis when |
groups |
A factor or character vector specifying group membership for each sample. If provided, the plot will be colored by group. Only applicable to "scores" and "loadings" types. |
group_col |
A character string specifying where to find the group information.
If you uses |
... |
Ignored. |
A ggplot object.
Visualization for glystats::gly_pca() results (glystats_pca_res object).
Possible types of plots:
"screeplot": Scree plot to see the contribution of each PC.
"individual" (default): Plot samples as individuals.
"variables": Plot loadings for variables.
"biplot": Biplot showing both samples and variables.
## S3 method for class 'glystats_pca_res' autoplot(object, type = "individual", groups = NULL, group_col = NULL, ...)## S3 method for class 'glystats_pca_res' autoplot(object, type = "individual", groups = NULL, group_col = NULL, ...)
object |
A |
type |
The type of plot, one of "screeplot", "individual", "variables", or "biplot". |
groups |
A factor or character vector specifying group membership for each sample.
If provided, the plot will be colored by group.
Only applicable to "individual" and "biplot" types.
Passed to the |
group_col |
A character string specifying where to find the group information.
If you uses |
... |
Other arguments passed to factoextra functions.
|
A ggplot object.
factoextra::fviz_screeplot(), factoextra::fviz_pca_ind(),
factoextra::fviz_pca_var(), factoextra::fviz_pca_biplot()
Visualization for results from glystats::gly_plsda() (glystats_plsda_res object).
Possible types of plots:
"scores" (default): Plot scores for samples.
"loadings": Plot loadings for variables.
"vip": Plot VIP scores for variables.
"variance": Plot explained variance for each component.
## S3 method for class 'glystats_plsda_res' autoplot(object, type = "scores", groups = NULL, group_col = NULL, ...)## S3 method for class 'glystats_plsda_res' autoplot(object, type = "scores", groups = NULL, group_col = NULL, ...)
object |
A |
type |
The type of plot, one of "loadings", "scores", "vip", or "variance". Defaults to "scores". |
groups |
A factor or character vector specifying group membership for each sample. If provided, the plot will be colored by group. Only applicable to "scores" and "loadings" types. |
group_col |
A character string specifying where to find the group information.
If you uses |
... |
Ignored. |
A ggplot object.
Visualization for results from glystats::gly_roc() (glystats_roc_res objects).
At most 10 variables can be plotted.
## S3 method for class 'glystats_roc_res' autoplot(object, type = "dotplot", auc_cutoff = 0.5, ...)## S3 method for class 'glystats_roc_res' autoplot(object, type = "dotplot", auc_cutoff = 0.5, ...)
object |
A |
type |
"dotplot" or "roc". Defaults to "dotplot". If "roc", at most 10 variables can be plotted. |
auc_cutoff |
The AUC cutoff. Defaults to 0.5. Only used if type is "dotplot". |
... |
Ignored. |
A ggplot object.
Visualization for results from glystats::gly_tsne() (glystats_tsne_res objects).
Draw a scatter plot of t-SNE coordinates.
## S3 method for class 'glystats_tsne_res' autoplot(object, groups = NULL, group_col = NULL, ...)## S3 method for class 'glystats_tsne_res' autoplot(object, groups = NULL, group_col = NULL, ...)
object |
A |
groups |
A factor or character vector specifying group membership for each sample. If provided, the plot will be colored by group. |
group_col |
A character string specifying where to find the group information.
If you uses |
... |
Ignored. |
A ggplot object.
Visualization for results from glystats::gly_ttest() and glystats::gly_wilcox()
(glystats_ttest_res and glystats_wilcox_res objects).
Draw a volcano plot.
## S3 method for class 'glystats_ttest_res' autoplot(object, log2fc_cutoff = 1, p_cutoff = 0.05, p_col = "p_adj", ...) ## S3 method for class 'glystats_wilcox_res' autoplot(object, log2fc_cutoff = 1, p_cutoff = 0.05, p_col = "p_adj", ...)## S3 method for class 'glystats_ttest_res' autoplot(object, log2fc_cutoff = 1, p_cutoff = 0.05, p_col = "p_adj", ...) ## S3 method for class 'glystats_wilcox_res' autoplot(object, log2fc_cutoff = 1, p_cutoff = 0.05, p_col = "p_adj", ...)
object |
A |
log2fc_cutoff |
The log2 fold change cutoff. Defaults to 1. |
p_cutoff |
The p-value cutoff. Defaults to 0.05. |
p_col |
The column name for p-value. Defaults to "p_adj". Can also be "p_val" (raw p-values without multiple testing correction). |
... |
Ignored. |
A ggplot object.
Visualization for results from glystats::gly_umap() (glystats_umap_res objects).
Draw a scatter plot of UMAP coordinates.
## S3 method for class 'glystats_umap_res' autoplot(object, groups = NULL, group_col = NULL, ...)## S3 method for class 'glystats_umap_res' autoplot(object, groups = NULL, group_col = NULL, ...)
object |
A |
groups |
A factor or character vector specifying group membership for each sample. If provided, the plot will be colored by group. |
group_col |
A character string specifying where to find the group information.
If you uses |
... |
Ignored. |
A ggplot object.
Draw a boxplot. Currently supported data types:
glyexp_experiment: Experiment created by glyexp::experiment().
Boxplots of log2-transformed expression values are plotted, grouped by the group column.
plot_boxplot(x, ...) ## S3 method for class 'glyexp_experiment' plot_boxplot(x, group_col = "group", ...)plot_boxplot(x, ...) ## S3 method for class 'glyexp_experiment' plot_boxplot(x, group_col = "group", ...)
x |
An object to be plotted. |
... |
Ignored. |
group_col |
A character string specifying the column name in sample information that contains group labels. Default is "group". |
A ggplot object.
Draw a correlation matrix heatmap. Currently supported data types:
glystats_cor_res: Result from glystats::gly_cor().
glyexp_experiment: Experiment created by glyexp::experiment().
Correlation analysis is first performed using glystats::gly_cor(),
then the result is plotted.
plot_corrplot(x, ...) ## S3 method for class 'glystats_cor_res' plot_corrplot(x, ...) ## S3 method for class 'glyexp_experiment' plot_corrplot(x, stats_args = list(), ...)plot_corrplot(x, ...) ## S3 method for class 'glystats_cor_res' plot_corrplot(x, ...) ## S3 method for class 'glyexp_experiment' plot_corrplot(x, stats_args = list(), ...)
x |
An object to be plotted. |
... |
Additional arguments passed to |
stats_args |
A list of keyword arguments to pass to |
A ggplot object.
Draw a enrichment analysis result plot. Currently supported data types:
glystats_go_ora_res: Result from glystats::gly_enrich_go().
glystats_kegg_ora_res: Result from glystats::gly_enrich_kegg().
glystats_reactome_ora_res: Result from glystats::gly_enrich_reactome().
glyexp_experiment: Experiment created by glyexp::experiment().
Enrichment analysis is first performed using glystats::gly_enrich_go(), glystats::gly_enrich_kegg(),
or glystats::gly_enrich_reactome(), then the result is plotted.
plot_enrich(x, type = "dotplot", ...) ## S3 method for class 'glystats_go_ora_res' plot_enrich(x, type = "dotplot", ...) ## S3 method for class 'glystats_kegg_ora_res' plot_enrich(x, type = "dotplot", ...) ## S3 method for class 'glystats_reactome_ora_res' plot_enrich(x, type = "dotplot", ...) ## S3 method for class 'glyexp_experiment' plot_enrich(x, type = "dotplot", enrich_type = "go", stats_args = list(), ...)plot_enrich(x, type = "dotplot", ...) ## S3 method for class 'glystats_go_ora_res' plot_enrich(x, type = "dotplot", ...) ## S3 method for class 'glystats_kegg_ora_res' plot_enrich(x, type = "dotplot", ...) ## S3 method for class 'glystats_reactome_ora_res' plot_enrich(x, type = "dotplot", ...) ## S3 method for class 'glyexp_experiment' plot_enrich(x, type = "dotplot", enrich_type = "go", stats_args = list(), ...)
x |
An object to be plotted. |
type |
The type of plot, one of "dotplot" (default), "barplot", or "network". |
... |
Additional arguments passed to underlying functions:
|
enrich_type |
The type of enrichment analysis, one of "go" (default), "kegg", or "reactome". |
stats_args |
A list of keyword arguments to pass to |
A ggplot object.
Draw a heatmap from a glyexp::experiment().
Heatmap of log2-transformed expression values is plotted.
Before plotting, zero-variance rows and columns are filtered out
to ensure robust clustering.
plot_heatmap(x, ...) ## S3 method for class 'glyexp_experiment' plot_heatmap(x, ...)plot_heatmap(x, ...) ## S3 method for class 'glyexp_experiment' plot_heatmap(x, ...)
x |
A |
... |
Other arguments passed to |
A ggplot object.
Draw a logo plot for all glycosites. Positions with insufficient flanking amino acids will be padded with "X". Currently supported data types:
glyexp_experiment: Experiment created by glyexp::experiment().
Logo plot of glycosylation sites is plotted.
plot_logo(x, n_aa = 5L, fasta = NULL, tax_id = 9606L, ...) ## S3 method for class 'glyexp_experiment' plot_logo(x, n_aa = 5L, fasta = NULL, tax_id = 9606L, ...)plot_logo(x, n_aa = 5L, fasta = NULL, tax_id = 9606L, ...) ## S3 method for class 'glyexp_experiment' plot_logo(x, n_aa = 5L, fasta = NULL, tax_id = 9606L, ...)
x |
An object to be plotted. |
n_aa |
The number of amino acids to the left and right of the glycosylation site.
For example, if |
fasta |
The path to the FASTA file containing protein sequences.
If |
tax_id |
The NCBI taxonomy ID used for UniProt.ws lookups. Defaults to 9606. |
... |
Additional arguments passed to |
A ggplot object.
Draw a OPLS-DA scores plot. Currently supported data types:
glystats_oplsda_res: Result from glystats::gly_oplsda().
glyexp_experiment: Experiment created by glyexp::experiment().
OPLS-DA analysis is first performed using glystats::gly_oplsda(),
then the result is plotted.
plot_oplsda( x, type = "scores", y_type = "o1", groups = NULL, group_col = NULL, ... ) ## S3 method for class 'glystats_oplsda_res' plot_oplsda( x, type = "scores", y_type = "o1", groups = NULL, group_col = NULL, ... ) ## S3 method for class 'glyexp_experiment' plot_oplsda( x, type = "scores", y_type = "o1", groups = NULL, group_col = NULL, stats_args = list(), ... )plot_oplsda( x, type = "scores", y_type = "o1", groups = NULL, group_col = NULL, ... ) ## S3 method for class 'glystats_oplsda_res' plot_oplsda( x, type = "scores", y_type = "o1", groups = NULL, group_col = NULL, ... ) ## S3 method for class 'glyexp_experiment' plot_oplsda( x, type = "scores", y_type = "o1", groups = NULL, group_col = NULL, stats_args = list(), ... )
x |
An object to be plotted. |
type |
The type of plot, one of "loadings", "scores", "vip", "variance", or "s-plot". Defaults to "scores". |
y_type |
What to plot on the y-axis when |
groups |
A factor or character vector specifying group membership for each sample. If provided, the plot will be colored by group. Only applicable to "scores" and "loadings" types. |
group_col |
A character string specifying where to find the group information.
If you uses |
... |
Ignored. |
stats_args |
A list of keyword arguments to pass to |
A ggplot object.
Draw a PCA scores plot. Currently supported data types:
glystats_pca_res: Result from glystats::gly_pca().
glyexp_experiment: Experiment created by glyexp::experiment().
PCA analysis is first performed using glystats::gly_pca(),
then the result is plotted.
plot_pca(x, type = "individual", groups = NULL, group_col = NULL, ...) ## S3 method for class 'glystats_pca_res' plot_pca(x, type = "individual", groups = NULL, group_col = NULL, ...) ## S3 method for class 'glyexp_experiment' plot_pca( x, type = "individual", groups = NULL, group_col = NULL, stats_args = list(), ... )plot_pca(x, type = "individual", groups = NULL, group_col = NULL, ...) ## S3 method for class 'glystats_pca_res' plot_pca(x, type = "individual", groups = NULL, group_col = NULL, ...) ## S3 method for class 'glyexp_experiment' plot_pca( x, type = "individual", groups = NULL, group_col = NULL, stats_args = list(), ... )
x |
An object to be plotted. |
type |
The type of plot, one of "screeplot", "individual", "variables", or "biplot". |
groups |
A factor or character vector specifying group membership for each sample.
If provided, the plot will be colored by group.
Only applicable to "individual" and "biplot" types.
Passed to the |
group_col |
A character string specifying where to find the group information. |
... |
Additional arguments passed to underlying factoextra functions:
|
stats_args |
A list of keyword arguments to pass to |
A ggplot object.
factoextra::fviz_screeplot(), factoextra::fviz_pca_ind(),
factoextra::fviz_pca_var(), factoextra::fviz_pca_biplot()
Draw a PLS-DA scores plot. Currently supported data types:
glystats_plsda_res: Result from glystats::gly_plsda().
glyexp_experiment: Experiment created by glyexp::experiment().
PLS-DA analysis is first performed using glystats::gly_plsda(),
then the result is plotted.
plot_plsda(x, type = "scores", groups = NULL, group_col = NULL, ...) ## S3 method for class 'glystats_plsda_res' plot_plsda(x, type = "scores", groups = NULL, group_col = NULL, ...) ## S3 method for class 'glyexp_experiment' plot_plsda( x, type = "scores", groups = NULL, group_col = NULL, stats_args = list(), ... )plot_plsda(x, type = "scores", groups = NULL, group_col = NULL, ...) ## S3 method for class 'glystats_plsda_res' plot_plsda(x, type = "scores", groups = NULL, group_col = NULL, ...) ## S3 method for class 'glyexp_experiment' plot_plsda( x, type = "scores", groups = NULL, group_col = NULL, stats_args = list(), ... )
x |
An object to be plotted. |
type |
The type of plot, one of "loadings", "scores", "vip", or "variance". Defaults to "scores". |
groups |
A factor or character vector specifying group membership for each sample. If provided, the plot will be colored by group. Only applicable to "scores" and "loadings" types. |
group_col |
A character string specifying where to find the group information.
If you uses |
... |
Ignored. |
stats_args |
A list of keyword arguments to pass to |
A ggplot object.
Draw ROC curves. Only two groups are allowed. At most 10 variables can be plotted. Currently supported data types:
glystats_roc_res: Result from glystats::gly_roc().
glyexp_experiment: Experiment created by glyexp::experiment().
ROC analysis is first performed using glystats::gly_roc(),
then the result is plotted.
plot_roc(x, type = "roc", auc_cutoff = 0.5, ...) ## S3 method for class 'glystats_roc_res' plot_roc(x, type = "roc", auc_cutoff = 0.5, ...) ## S3 method for class 'glyexp_experiment' plot_roc(x, type = "roc", auc_cutoff = 0.5, stats_args = list(), ...)plot_roc(x, type = "roc", auc_cutoff = 0.5, ...) ## S3 method for class 'glystats_roc_res' plot_roc(x, type = "roc", auc_cutoff = 0.5, ...) ## S3 method for class 'glyexp_experiment' plot_roc(x, type = "roc", auc_cutoff = 0.5, stats_args = list(), ...)
x |
An object to be plotted. |
type |
The type of plot, one of "dotplot" or "roc". Default is "roc". |
auc_cutoff |
The AUC cutoff. Default is 0.5. |
... |
Ignored. |
stats_args |
A list of keyword arguments to pass to |
A ggplot object.
Draw a t-SNE scores plot. Currently supported data types:
glystats_tsne_res: Result from glystats::gly_tsne().
glyexp_experiment: Experiment created by glyexp::experiment().
t-SNE analysis is first performed using glystats::gly_tsne(),
then the result is plotted.
plot_tsne(x, ...) ## S3 method for class 'glystats_tsne_res' plot_tsne(x, groups = NULL, group_col = NULL, ...) ## S3 method for class 'glyexp_experiment' plot_tsne(x, groups = NULL, group_col = NULL, stats_args = list(), ...)plot_tsne(x, ...) ## S3 method for class 'glystats_tsne_res' plot_tsne(x, groups = NULL, group_col = NULL, ...) ## S3 method for class 'glyexp_experiment' plot_tsne(x, groups = NULL, group_col = NULL, stats_args = list(), ...)
x |
An object to be plotted. |
... |
Ignored. |
groups |
A factor or character vector specifying group membership for each sample. If provided, the plot will be colored by group. |
group_col |
A character string specifying where to find the group information.
If you uses |
stats_args |
A list of keyword arguments to pass to |
A ggplot object.
Draw a UMAP scores plot. Currently supported data types:
glystats_umap_res: Result from glystats::gly_umap().
glyexp_experiment: Experiment created by glyexp::experiment().
UMAP analysis is first performed using glystats::gly_umap(),
then the result is plotted.
plot_umap(x, ...) ## S3 method for class 'glystats_umap_res' plot_umap(x, groups = NULL, group_col = NULL, ...) ## S3 method for class 'glyexp_experiment' plot_umap(x, groups = NULL, group_col = NULL, stats_args = list(), ...)plot_umap(x, ...) ## S3 method for class 'glystats_umap_res' plot_umap(x, groups = NULL, group_col = NULL, ...) ## S3 method for class 'glyexp_experiment' plot_umap(x, groups = NULL, group_col = NULL, stats_args = list(), ...)
x |
An object to be plotted. |
... |
Ignored. |
groups |
A factor or character vector specifying group membership for each sample. If provided, the plot will be colored by group. |
group_col |
A character string specifying where to find the group information.
If you uses |
stats_args |
A list of keyword arguments to pass to |
A ggplot object.
Draw a volcano plot. Currently supported data types:
glystats_ttest_res: Result from glystats::gly_ttest().
glystats_wilcox_res: Result from glystats::gly_wilcox().
glystats_limma_res: Result from glystats::gly_limma().
Only two-group comparisons are supported.
glyexp_experiment: Experiment created by glyexp::experiment().
Differential expression analysis is first performed using glystats::gly_ttest(),
glystats::gly_wilcox(), or glystats::gly_limma()
(controlled by the test argument), then the result is plotted.
plot_volcano(x, log2fc_cutoff = 1, p_cutoff = 0.05, p_col = "p_adj", ...) ## S3 method for class 'glyexp_experiment' plot_volcano( x, log2fc_cutoff = 1, p_cutoff = 0.05, p_col = "p_adj", test = "limma", stats_args = list(), ... ) ## S3 method for class 'glystats_ttest_res' plot_volcano(x, log2fc_cutoff = 1, p_cutoff = 0.05, p_col = "p_adj", ...) ## S3 method for class 'glystats_wilcox_res' plot_volcano(x, log2fc_cutoff = 1, p_cutoff = 0.05, p_col = "p_adj", ...) ## S3 method for class 'glystats_limma_res' plot_volcano( x, log2fc_cutoff = 1, p_cutoff = 0.05, p_col = "p_adj", contrast = NULL, ... )plot_volcano(x, log2fc_cutoff = 1, p_cutoff = 0.05, p_col = "p_adj", ...) ## S3 method for class 'glyexp_experiment' plot_volcano( x, log2fc_cutoff = 1, p_cutoff = 0.05, p_col = "p_adj", test = "limma", stats_args = list(), ... ) ## S3 method for class 'glystats_ttest_res' plot_volcano(x, log2fc_cutoff = 1, p_cutoff = 0.05, p_col = "p_adj", ...) ## S3 method for class 'glystats_wilcox_res' plot_volcano(x, log2fc_cutoff = 1, p_cutoff = 0.05, p_col = "p_adj", ...) ## S3 method for class 'glystats_limma_res' plot_volcano( x, log2fc_cutoff = 1, p_cutoff = 0.05, p_col = "p_adj", contrast = NULL, ... )
x |
An object to be plotted. |
log2fc_cutoff |
The log2 fold change cutoff. Defaults to 1. |
p_cutoff |
The p-value cutoff. Defaults to 0.05. |
p_col |
The column name for p-value. Defaults to "p_adj". Can also be "p_val" (raw p-values without multiple testing correction). |
... |
Other arguments passed to |
test |
"ttest", "wilcox", or "limma". Default is "limma". |
stats_args |
A list of keyword arguments to pass to |
contrast |
A character string specifying the contrast to plot, in the format of "group1_vs_group2". Must be one of the contrasts in the result. When there is only one contrast (two-group comparison), it can be NULL (default). |
A ggplot object.