gseaNb: gseaNb

Description

gseaNb

Value

ggplot2 object

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.

Author

Jun Zhang

Examples

Run this code

# 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)

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