Title: | Implement for 'GSEA' Enrichment Visualization |
---|---|
Description: | Mark your interesting genes on plot and support more parameters to handle your own gene set enrichment analysis plot. |
Authors: | Jun Zhang [aut, cre] , Guangchuang Yu [ctb] |
Maintainer: | Jun Zhang <[email protected]> |
License: | MIT + file LICENSE |
Version: | 0.1.0 |
Built: | 2024-03-24 08:01:03 UTC |
Source: | https://github.com/junjunlab/gseavis |
This function creates a gseaResult object from the results of enrichment analysis using gene set enrichment analysis (GSEA) for a given gene list and Gene Ontology (GO) data.
dfGO2gseaResult(
enrich.df = NULL,
geneList = NULL,
OrgDb = NULL,
keytype = "ENTREZID",
setType = c("BP", "CC", "MF", "ALL"),
pvalueCutoff = 0.05,
eps = 1e-10,
pAdjustMethod = "BH",
exponent = 1,
minGSSize = 120,
maxGSSize = 500
)
enrich.df |
A data frame containing the results of enrichment analysis. |
geneList |
A decreasing sorted vector of gene list. |
OrgDb |
The organism-specific annotation database. |
keytype |
The type of gene identifier used in the analysis (default is "ENTREZID"). |
setType |
The type of GO ontology to use ("BP" for Biological Process, "CC" for Cellular Component, "MF" for Molecular Function, or "ALL" for all ontologies). |
pvalueCutoff |
The p-value cutoff for significance (default is 0.05). |
eps |
A small value to avoid division by zero (default is 1e-10). |
pAdjustMethod |
The p-value adjustment method (default is "BH" for Benjamini-Hochberg). |
exponent |
The exponent for weighting p-values (default is 1). |
minGSSize |
The minimum gene set size (default is 120). |
maxGSSize |
The maximum gene set size (default is 500). |
A gseaResult object containing the results of GSEA.
This function creates a gseaResult object from the results of KEGG enrichment analysis for a given gene list and organism.
dfKEGG2gseaResult(
enrich.df = NULL,
geneList = NULL,
organism = "hsa",
keytype = "kegg",
setType = "KEGG",
use_internal_data = FALSE,
pvalueCutoff = 0.05,
eps = 1e-10,
pAdjustMethod = "BH",
exponent = 1,
minGSSize = 120,
maxGSSize = 500
)
enrich.df |
A data frame containing the results of KEGG enrichment analysis. |
geneList |
A decreasing sorted vector of gene identifiers. |
organism |
The organism for KEGG enrichment analysis (default is "hsa" for Homo sapiens). |
keytype |
The type of gene identifier used in the analysis (default is "kegg"). |
setType |
The type of enrichment analysis ("KEGG" for KEGG pathways). |
use_internal_data |
Logical value indicating whether to use internal KEGG data (default is FALSE). |
pvalueCutoff |
The p-value cutoff for significance (default is 0.05). |
eps |
A small value to avoid division by zero (default is 1e-10). |
pAdjustMethod |
The p-value adjustment method (default is "BH" for Benjamini-Hochberg). |
exponent |
The exponent for weighting p-values (default is 1). |
minGSSize |
The minimum gene set size (default is 120). |
maxGSSize |
The maximum gene set size (default is 500). |
A gseaResult object containing the results of KEGG enrichment analysis.
dotplotGsea
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". |
a ggplot object.
Jun Zhang
This function generates a multi-group plot for Gene Set Enrichment Analysis (GSEA) results.
GSEAmultiGP(
gsea_list = NULL,
geneSetID = NULL,
exp_name = NULL,
addPval = FALSE,
curve.col = NULL,
curve.linewidth = 1,
kegg = FALSE,
lineSize = 1,
base_size = 12,
nesDigit = 2,
pDigit = 2,
pvalX = 0.9,
pvalY = 0.9,
rect.bm.col = c("#CC3333", "white", "#003366"),
subplot.heights = c(0.4, 0.2, 0.08),
legend.position = c(0.85, 0.85),
rect.bm.label = c("Up regulated", "Down regulated"),
breaks.n = 6
)
gsea_list |
A list of GSEA results for multiple experiments. |
geneSetID |
The ID of the gene set to be visualized. |
exp_name |
Names of the experiments corresponding to the GSEA results. |
addPval |
Logical, indicating whether to add NES (Normalized Enrichment Score) and p-value labels to the plot. Default is FALSE. |
curve.col |
A vector of colors for the curves representing different experiments. If NULL, random colors are assigned. |
curve.linewidth |
The curve linewidth. Default is 1. |
kegg |
Logical, indicating whether the gene set is a KEGG pathway. Default is FALSE. |
lineSize |
The size of the lines in the enrichment score curve plot. Default is 1. |
base_size |
The base font size for the plot. Default is 12. |
nesDigit |
The number of digits to round NES values to. Default is 2. |
pDigit |
The number of digits to round p-values to. Default is 2. |
pvalX |
The X-coordinate for placing p-value labels on the plot. Default is 0.9. |
pvalY |
The Y-coordinate for placing p-value labels on the plot. Default is 0.9. |
rect.bm.col |
A vector of colors for the bottom rectangle representing up-regulated and down-regulated genes. Default colors c("#CC3333","white","#003366") are provided. |
subplot.heights |
Heights of subplots in the multi-group plot. Default values c(0.4,0.2,0.08) are provided. |
legend.position |
The position of the legend in the plot. Default is (0.85, 0.85). |
rect.bm.label |
Labels for the bottom rectangle, specifying "Up regulated" and "Down regulated". Default labels are provided. |
breaks.n |
The number of X axis breaks. Default is 6. |
Returns a multi-panel plot for GSEA results.
Jun Zhang
## Not run:
# Example Usage
result <- GSEAmultiGP(gsea_list = gsea_results,
geneSetID = "gene_set_1",
exp_name = c("Exp1", "Exp2"),
addPval = TRUE,
curve.col = c("red", "blue"),
pvalX = 0.9,
pvalY = 0.9,
rect.bm.col = c("#CC3333", "white", "#003366"),
subplot.heights = c(0.4, 0.2, 0.08),
legend.position = c(0.85, 0.85),
rect.bm.label = c("Up regulated", "Down regulated"))
## End(Not run)
gseaNb
object |
GSEA enrich results. |
filePath |
filePath the path of the GSEA software enrichment outputs or "readGseaFile" object, defalut is NULL. |
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. |
rm.newGsea.ticks |
whether remove right axis when you plot multiple terms with newGsea plot, defalut is TRUE. |
pFill |
the pvalue table fill color when you plot multiple terms with newGsea plot, defalut is transparent. |
base_size |
the plot theme font size, defalut is 12. |
ncol |
the columns for newGSEA plot with multiple terms, defalut is 1 |
ggplot2 object
Jun Zhang
# 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)
gsInfo
gsInfo(object, geneSetID)
object |
gseaResult object |
geneSetID |
gene set ID |
data.frame
Guangchuang Yu
gsInfoNew
gsInfoNew(geneList = NULL, geneSetID = NULL, geneSet = NULL, exponent = 1)
geneList |
geneList for GSEA software outputs which is saved in "gseaOutputs/ranked_gene_list_treat_versus_control*.tsv". |
geneSetID |
gene set ID. |
geneSet |
enrichment term sets for GSEA software outputs which is saved in "*/edb/gene_sets". |
exponent |
weight of each step, defalut is 1. |
a data.frame
Guangchuang Yu, modified by JunZhang
This is a test data for this package test data describtion
intergrated
An object of class list
of length 3.
JunZhang
readGseaFile
filePath |
the path of the GSEA software enrichment outputs, defalut is NULL. |
a list contains meta(intergated enrichment results), glist(the ordered gene lists), gset(all background enrichment terms).
volcanoGsea
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"),
...
)
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. |
a ggplot object.
Jun Zhang