| gseaNb {GseaVis} | R Documentation |
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)