This function generates various types of plots for Gene Set Enrichment Analysis (GSEA) results.
Usage
GSEAPlot(
srt,
db = "GO_BP",
group_by = NULL,
test.use = "wilcox",
res = NULL,
plot_type = c("line", "bar", "network", "enrichmap", "wordcloud", "comparison"),
group_use = NULL,
id_use = NULL,
pvalueCutoff = NULL,
padjustCutoff = 0.05,
topTerm = ifelse(plot_type == "enrichmap", 100, 6),
direction = c("pos", "neg", "both"),
compare_only_sig = FALSE,
topWord = 100,
word_type = c("term", "feature"),
word_size = c(2, 8),
words_excluded = NULL,
line_width = 1.5,
line_alpha = 1,
line_color = "#6BB82D",
n_coregene = 10,
sample_coregene = FALSE,
features_label = NULL,
label.fg = "black",
label.bg = "white",
label.bg.r = 0.1,
label.size = 4,
network_layout = "fr",
network_labelsize = 5,
network_blendmode = "blend",
network_layoutadjust = TRUE,
network_adjscale = 60,
network_adjiter = 100,
enrichmap_layout = "fr",
enrichmap_cluster = "fast_greedy",
enrichmap_label = c("term", "feature"),
enrichmap_labelsize = 5,
enrlichmap_nlabel = 4,
enrichmap_show_keyword = FALSE,
enrichmap_mark = c("ellipse", "hull"),
enrichmap_expand = c(0.5, 0.5),
character_width = 50,
lineheight = 0.5,
palette = "Spectral",
palcolor = NULL,
aspect.ratio = NULL,
legend.position = "right",
legend.direction = "vertical",
theme_use = "theme_scop",
theme_args = list(),
combine = TRUE,
nrow = NULL,
ncol = NULL,
byrow = TRUE,
seed = 11
)
Arguments
- srt
A Seurat object containing the results of RunDEtest and RunGSEA. If specified, GSEA results will be extracted from the Seurat object automatically. If not specified, the
res
arguments must be provided.- db
The database to use for enrichment plot. Default is
"GO_BP"
.- group_by
A character vector specifying the grouping variable in the
Seurat
object. This argument is only used ifsrt
is specified.- test.use
A character vector specifying the test to be used in differential expression analysis. This argument is only used if
srt
is specified.- res
Enrichment results generated by RunGSEA function. If provided, 'srt', 'test.use' and 'group_by' are ignored.
- plot_type
The type of plot to generate. Options are: "line", "comparison", "bar", "network", "enrichmap", "wordcloud". Default is "line".
- group_use
The group(s) to be used for enrichment plot. Default is
NULL
.- id_use
List of IDs to be used to display specific terms in the enrichment plot. Default value is
NULL
.- pvalueCutoff
The p-value cutoff. Only work when
padjustCutoff
isNULL
. Default isNULL
.- padjustCutoff
The p-adjusted cutoff. Default is
0.05
.- topTerm
The number of top terms to display. Default is 6, or 100 if
plot_type
is"enrichmap"
.- direction
The direction of enrichment to include in the plot. Must be one of "pos", "neg", or "both". The default value is "both".
- compare_only_sig
Whether to compare only significant terms. Default is
FALSE
.- topWord
The number of top words to display for wordcloud. Default is
100
.- word_type
The type of words to display in wordcloud. Options are
"term"
and"feature"
. Default is"term"
.- word_size
The size range for words in wordcloud. Default is
c(2, 8)
.- words_excluded
Words to be excluded from the wordcloud. The default value is
NULL
, which means that the built-in words (words_excluded) will be used.- line_width
The linewidth for the line plot.
- line_alpha
The alpha value for the line plot.
- line_color
The color for the line plot.
- n_coregene
The number of core genes to label in the line plot.
- sample_coregene
Whether to randomly sample core genes for labeling in the line plot.
- features_label
A character vector of feature names to include as labels in the line plot.
- label.fg
The color of the labels.
- label.bg
The background color of the labels.
- label.bg.r
The radius of the rounding of the label's background.
- label.size
The size of the labels.
- network_layout
The layout algorithm to use for network plot. Options are
"fr"
,"kk"
,"random"
,"circle"
,"tree"
,"grid"
, or other algorithm fromigraph
package. Default is"fr"
.- network_labelsize
The label size for network plot. Default is
5
.- network_blendmode
The blend mode for network plot. Default is
"blend"
.- network_layoutadjust
Whether to adjust the layout of the network plot to avoid overlapping words. Default is
TRUE
.- network_adjscale
The scale for adjusting network plot layout. Default is
60
.- network_adjiter
The number of iterations for adjusting network plot layout. Default is
100
.- enrichmap_layout
The layout algorithm to use for enrichmap plot. Options are
"fr"
,"kk"
,"random"
,"circle"
,"tree"
,"grid"
, or other algorithm fromigraph
package. Default is"fr"
.- enrichmap_cluster
The clustering algorithm to use for enrichmap plot. Options are
"walktrap"
,"fast_greedy"
, or other algorithm fromigraph
package. Default is"fast_greedy"
.- enrichmap_label
The label type for enrichmap plot. Options are
"term"
and"feature"
. Default is"term"
.- enrichmap_labelsize
The label size for enrichmap plot. Default is
5
.- enrlichmap_nlabel
The number of labels to display for each cluster in enrichmap plot. Default is
4
.- enrichmap_show_keyword
Whether to show the keyword of terms or features in enrichmap plot. Default is
FALSE
.- enrichmap_mark
The mark shape for enrichmap plot. Options are
"ellipse"
and"hull"
. Default is"ellipse"
.- enrichmap_expand
The expansion factor for enrichmap plot. Default is
c(0.5, 0.5)
.- character_width
The maximum width of character of descriptions. Default is
50
.- lineheight
The line height for y-axis labels. Default is
0.5
.- palette
The color palette to use. Default is
"Spectral"
.- palcolor
Custom colors for palette. Default is
NULL
.- aspect.ratio
The aspect ratio of the plot. Default is
1
.- legend.position
The position of the legend. Default is
"right"
.- legend.direction
The direction of the legend. Default is
"vertical"
.- theme_use
The theme to use for the plot. Default is
"theme_scop"
.- theme_args
The arguments to pass to the theme. Default is an empty list.
- combine
Whether to combine multiple plots into a single plot. Default is
TRUE
.- nrow
The number of rows in the combined plot. Default is NULL, calculated based on the number of plots.
- ncol
The number of columns in the combined plot. Default is NULL, calculated based on the number of plots.
- byrow
Whether to fill the combined plot by row. Default is
TRUE
.- seed
The random seed to use. Default is
11
.
Examples
if (FALSE) { # \dontrun{
data(pancreas_sub)
pancreas_sub <- standard_scop(pancreas_sub)
pancreas_sub <- RunDEtest(
pancreas_sub,
group_by = "CellType"
)
pancreas_sub <- RunGSEA(
pancreas_sub,
group_by = "CellType",
db = "GO_BP",
species = "Mus_musculus"
)
GSEAPlot(
pancreas_sub,
db = "GO_BP",
group_by = "CellType",
group_use = "Ductal"
)
p1 <- GSEAPlot(
pancreas_sub,
db = "GO_BP",
group_by = "CellType",
group_use = "Ductal",
id_use = "GO:0006412"
)
p1
panel_fix_overall(p1, height = 6)
GSEAPlot(
pancreas_sub,
db = "GO_BP",
group_by = "CellType",
topTerm = 3,
plot_type = "comparison"
)
GSEAPlot(
pancreas_sub,
db = "GO_BP",
group_by = "CellType",
topTerm = 3,
plot_type = "comparison",
direction = "pos"
)
GSEAPlot(
pancreas_sub,
db = "GO_BP",
group_by = "CellType",
topTerm = 3,
plot_type = "comparison",
compare_only_sig = TRUE
)
GSEAPlot(
pancreas_sub,
db = "GO_BP",
group_by = "CellType",
plot_type = "bar"
)
GSEAPlot(
pancreas_sub,
db = "GO_BP",
group_by = "CellType",
plot_type = "bar",
direction = "both"
)
GSEAPlot(
pancreas_sub,
db = "GO_BP",
group_by = "CellType",
group_use = "Ductal",
plot_type = "bar",
topTerm = 20,
direction = "both",
palcolor = c("red3", "steelblue")
)
GSEAPlot(
pancreas_sub,
db = "GO_BP",
group_by = "CellType",
group_use = "Ductal",
plot_type = "network"
)
GSEAPlot(
pancreas_sub,
db = "GO_BP",
group_by = "CellType",
group_use = "Ductal",
plot_type = "enrichmap"
)
GSEAPlot(
pancreas_sub,
db = "GO_BP",
group_by = "CellType",
group_use = "Ductal",
plot_type = "wordcloud"
)
GSEAPlot(
pancreas_sub,
db = "GO_BP",
group_by = "CellType",
group_use = "Ductal",
plot_type = "wordcloud",
word_type = "feature"
)
} # }