| Title: | Implement for 'GSEA' Enrichment Visualization |
| Version: | 0.0.5 |
| Maintainer: | Jun Zhang <3219030654@stu.cpu.edu.cn> |
| Description: | Mark your interesting genes on plot and support more parameters to handle your own gene set enrichment analysis plot. |
| License: | MIT + file LICENSE |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.2.1 |
| Imports: | aplot, DOSE, dplyr, ggplot2, ggpp, ggrepel, ggsci, grDevices, magrittr, purrr, RColorBrewer, reshape2, stringr, tibble, utils |
| URL: | https://github.com/junjunlab/GseaVis |
| BugReports: | https://github.com/junjunlab/GseaVis/issues |
| NeedsCompilation: | no |
| Packaged: | 2022-12-20 13:11:44 UTC; admin |
| Author: | Jun Zhang  [aut,
cre],
Guangchuang Yu [ctb] |
| Depends: | R (≥ 3.5.0) |
| Repository: | CRAN |
| Date/Publication: | 2022-12-20 19:40:07 UTC |
Pipe operator
Description
See magrittr::%>% for details.
Usage
lhs %>% rhs
Arguments
lhs |
A value or the magrittr placeholder. |
rhs |
A function call using the magrittr semantics. |
Value
The result of calling rhs(lhs).
dotplotGsea
Description
dotplotGsea
Arguments
data |
GSEA enrich object from clusterProfiler, defalut is NULL. |
pval |
pvalue cutoff to select significant terms, defalut is NULL. |
pajust |
adjusted pvalue cutoff to select significant terms, defalut is 0.05. |
order.by |
the X axis, defalut is "GeneRatio". |
str.width |
the width of term name, defalut is 50. |
base_size |
theme base size, defalut is 12. |
topn |
show the top terms, defalut is NULL. |
scales |
facet scales, defalut is "free_x". |
add.seg |
whether add segment line to point, defalut is "FALSE". |
line.col |
segment line color, defalut is "grey80". |
line.size |
segment line size, defalut is 1.5. |
line.type |
segment line type, defalut is "solid". |
Value
a ggplot object.
Author(s)
Jun Zhang
gsInfo
Description
gsInfo
Usage
gsInfo(object, geneSetID)
Arguments
object |
gseaResult object |
geneSetID |
gene set ID |
Value
data.frame
Author(s)
Guangchuang Yu
gseaNb
Description
gseaNb
Arguments
object |
GSEA enrich results. |
subPlot |
which plot to show, 1/2/3, default is 3. |
lineSize |
curve line size. default is 0.8. |
geneSetID |
which pathway name to plot. |
rmSegment |
whether to remove segment on the curve plot, default is FALSE. |
termWidth |
the width or the term name, defalut is 40. |
segCol |
segment color on the curves, defalut is "red". |
addGene |
whether add gene name on the curve, defalut is FALSE. |
geneCol |
gene name label color, defalut is NULL. |
arrowAngle |
arrow angle, defalut is 20. |
arrowLength |
arrow line length, defalut is 0.2. |
arrowEnd |
arrow end, defalut is "last". |
arrowType |
arrow type, defalut is "closed". |
curveCol |
curve color, defalut is c("#76BA99", "#EB4747", "#996699"). |
htCol |
heatmap color, defalut is c("#08519C", "#A50F15"). |
rankCol |
gene rank fill color, defalut is c("#08519C", "white", "#A50F15"). |
rankSeq |
gene rank plot X axis breaks, defalt is 5000. |
htHeight |
the relative height when "subplot = 2" to the vertical line plot, defalut is 0.3. |
force |
the gene label force, refer to geom_text_repel function, defalut is 20. |
max.overlaps |
refer to geom_text_repel function, defalut is 50. |
geneSize |
gene label text size, defalut is 4. |
newGsea |
whether show new style of plot, defalut is FALSE. |
addPoint |
new style plot with point layer, defalut is TRUE. |
newCurveCol |
new style plot curve color, defalut is c("#336699", "white", "#993399"). |
newHtCol |
new style plot heatmap color, defalut is c("#336699", "white", "#993399"). |
rmHt |
whether remove new style plot heatmap, defalut is FALSE. |
addPval |
whether add pvalue and NES, defalut is FALSE. |
pvalX |
set pvalue label x position, defalut is 0.9. |
pvalY |
set pvalue label y position, defalut is 0.9. |
pvalSize |
set pvalue label text size, defalut is 4. |
pCol |
pvalue label color, defalut is "grey30". |
pHjust |
pvalue label hjust, defalut is 1. |
rmPrefix |
whether remove GO term prefix like "GOBP/KEGG/CC/MF_*", defalut is TRUE. |
nesDigit |
the NES score digits retained, defalut is 2. |
pDigit |
the pvalue and pajust value digits retained, defalut is 2. |
markTopgene |
whether add top n genes on plot, defalut is FALSE. |
topGeneN |
the number of genes to be marked on plot, defalut is 5. |
kegg |
whether input is gseKEGG object, defalut is FALSE. |
legend.position |
the legend position, defalut is "right". |
whether |
add target gene expression heatmap, defalut is FALSE. |
exp |
the expression matrix,tpm/fpkm/rpkm format, defalut is NULL. |
scale.exp |
whether scale the expression matrix, defalut is TRUE. |
sample.order |
the expression matrix sample orders, defalut is NULL. |
exp.col |
the expression colors, defalut is c('blue','white','red'). |
ht.legend |
whether show the heatmap legend, defalut is TRUE. |
ght.relHight |
the relative height to the main plot, defalut is 0.4. |
ght.geneText.size |
the gene lable text size, defalut is 6. |
ght.facet |
whether facet expression heatmap, defalut is FALSE. |
ght.facet.scale |
the facet plot scale argumrnt, defalut is "free". |
termID.order |
the facet term ID orders, defalut is NULL. |
rank.gene |
add your gene label on rank plot, defalut is NULL. |
rank.gene.nudgey |
the gene label nudge y on rank plot, defalut is 2. |
Value
ggplot2 object
Author(s)
Jun Zhang
Examples
# load data
test_data <- system.file("extdata", "gseaRes.RDS", package = "GseaVis")
gseaRes <- readRDS(test_data)
# all plot
gseaNb(object = gseaRes,
geneSetID = 'GOBP_NUCLEOSIDE_DIPHOSPHATE_METABOLIC_PROCESS',
subPlot = 2)
volcanoGsea
Description
volcanoGsea
Usage
volcanoGsea(
data = NULL,
NES.cutoff = 1,
pvalue.cutoff = NULL,
p.adjust.CUTOFF = 0.05,
nudge.y = c(0, 0),
topN = 5,
point.size = 3,
point.color = c("#CC3333", "#CCCCCC", "#0099CC"),
...
)
Arguments
data |
GSEA enrich object from clusterProfiler, defalut is NULL. |
NES.cutoff |
NES cutoff to select significant terms, defalut is 1. |
pvalue.cutoff |
pvalue cutoff to select significant terms, defalut is NULL. |
p.adjust.CUTOFF |
adjusted pvalue cutoff to select significant terms, defalut is 0.05. |
nudge.y |
y shift to ajust label, defalut is c(0,0). |
topN |
top term to show, defalut is 5. |
point.size |
point size, defalut is 3. |
point.color |
point color, defalut is c('#CC3333','#CCCCCC','#0099CC'). |
... |
other arguments passed by geom_text_repel. |
Value
a ggplot object.
Author(s)
Jun Zhang