plotGseaDotPlot | R Documentation |
Visualizes results of gene set enrichment analysis with dot plots.
plotGseaDotPlot(
object,
across = getDefaultGrouping(object, verbose = TRUE, "across"),
across_subset = NULL,
relevel = NULL,
method_de = NULL,
by_group = TRUE,
n_gsets = 20,
signif_var = "fdr",
signif_threshold = 0.05,
alpha_by = NULL,
alpha_trans = "reverse",
color_by = "fdr",
color_trans = "reverse",
size_by = "fdr",
size_trans = "reverse",
pt_alpha = 0.9,
pt_size = 2,
pt_color = "blue4",
pt_clrsp = "plasma",
force_gsets = NULL,
force_opt = "add",
remove = "^.+?(?=_)",
remove_gsets = NULL,
replace = c("_", " "),
arrange_gsets = TRUE,
reverse = TRUE,
reverse_within = FALSE,
scientific = TRUE,
scales = "free",
nrow = NULL,
ncol = NULL,
transform_with = NULL,
verbose = NULL,
...
)
object |
An object of class |
across |
Character value or NULL. Specifies the grouping variable of interest. Use |
across_subset |
Character vector or NULL. Specifies the particular groups
of interest the grouping variable specified in argument If set to NULL all of them are chosen. You can prefix groups you are NOT interested in with a '-'. (Saves writing if there are more groups you are interested in than groups you are not interested in.) Use |
relevel |
Logical value. If set to TRUE the input order of |
method_de |
Character value. Denotes the method to according to which the de-analysis is performed.
Given to argument |
by_group |
Logical value. If TRUE for every group in the grouping variable a single dot plot is created. If FALSE one plot for all groups and all gene sets is created. |
n_gsets |
Numeric value. Maximal number of gene sets whose results are included.
The first |
signif_var |
Character value. Determines what to be considered while checking for significance. Either 'pval' (p-Value) or 'fdr' (False Discovery Rate). |
signif_threshold |
Numeric value. Significance values below |
pt_alpha |
Numeric value. Specifies the degree of transparency of all points. |
pt_size |
Numeric value. Specifies the size of all points. |
pt_clrsp |
The color spectrum to be used if the specified variable displayed by
color is continuous. Run |
remove |
Character value or NULL. If character, regular expression given
to |
remove_gsets |
Character value or NULL. If character, regular expression. All gene set names that match the regular expression are not included in the plot. |
replace |
Character vector of length 2 or NULL. If character vector, two regular expressions.
First value is given to argument |
arrange_gsets |
Logical. If TRUE gene sets are arranged by their group belonging. Making the appearance of the plots tidier. |
reverse |
Logical. If TRUE the gene sets are arranged from top to bottom. If FALSE they are arranged from bottom to top. |
nrow , ncol |
Numeric values or NULL. Used to arrange multiple plots. |
transform_with |
List or NULL. If list, can be used to transform continuous variables before plotting.
Names of the list slots refer to the variable. The content of the slot refers to the transforming functions.
Slot content can either be a character vector of function names. Use Useful if you want to apply more than one transformation on variables mapped to
plotting aesthetics. Input for |
verbose |
Logical. If set to TRUE informative messages regarding the computational progress will be printed. (Warning messages will always be printed.) |
... |
Used to absorb deprecated arguments or functions. |
reverse_whitin |
Logical. If TRUE the gene sets are displayed in a reversed order within the groups. |
A ggplot.
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