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 ORCID iD [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