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This article mainly introduces the relevant knowledge of "how to draw GO string diagram in R language". The editor shows you the operation process through an actual case. The operation method is simple, fast and practical. I hope this article "how to draw GO string diagram in R language" can help you solve the problem.

R packet GOplot visualizes the results of GO enrichment analysis and draws string diagrams.

Usage: $Rscript $scriptdir/GOChord_plot.r-husage: / share/nas1/fangs/test/Ferroptosis-Related/TCGA-ESCC/scripts/GOChord_plot.r [- h]-g GO_DATA-d DEG_DATA [--no_logFC] [--gene GENE] [--GO GO] [- z GENE_SIZE] [- S GENE_SPACE] [- s GO_SPACE] [- t TITLE] [- o OUTDIR] [- p PREFIX] [- H HEIGHT] [- W WIDTH] GOChord plot: https://www..com/article/1532optional arguments:-h -- help show this help message and exit-g GO_DATA,-- GO_data GO_DATA input a GO enrichment analysis data,the data with columns for 'category','ID','term',adjusted p-value (' adj_pval') and 'genes' [required]-d DEG_DATA -- deg_data DEG_DATA input the result of differential expression analysis corresponding to GO enrichment analysis,the data with columns for 'ID',' logFC' [required]-- no_logFC There is no logFC value [optional,default False]-- gene GENE The number of GOterms associated with a gene [optional Default 3]-- GO GO The number of genes associated with a GOterms [optional,default 5]-z GENE_SIZE,-- gene_size GENE_SIZE The size of the gene name [optional,default 5]-S GENE_SPACE,-- gene_space GENE_SPACE The spacing between genes [optional,default 0.25]-s GO_SPACE -- GO_space GO_SPACE The spacing between GOterms [optional,default 0.02]-t TITLE,-- title TITLE the title of the String figure [optional,default GOChord_plot]-o OUTDIR,-- outdir OUTDIR output file directory [optional,default cwd]-p PREFIX -- prefix PREFIX out file name prefix [optional,default GOChord_plot]-H HEIGHT,-- height HEIGHT the height of the String figure [optional,default 18]-W WIDTH,-- width WIDTH the width of the String figure [optional,default 20] parameter description:

-g enter the GO enrichment analysis result file, whose columns must contain "category" (BP/CC/MF),''ID "(GO ID)," term "(function description)," adj_pval "(corrected p value) and" genes "(gene ID contained in each GO term):

Category

ID

Term

GeneRatio

BgRatio

Pvalue

Adj_pval

Qvalue

Genes

Count

BPGO:0006979

Response to oxidative stress

10/37

458/18866

1.25E-08

1.79E-05

1.27E-05

TXNIP/FANCD2/ANGPTL7/NOX4/NCF2/HSPB1/PRKAA2/G6PD/TNFAIP3/HBA1

10BPGO:0062197

Cellular response to chemical stress

8/37

360/18866

3.87E-07

0.0002770.000198

FANCD2/SLC2A1/NOX4/NCF2/HSPB1/PRKAA2/G6PD/TNFAIP3

8BPGO:0001894

Tissue homeostasis

7/37

261/18866

6.46E-07

0.0003080.000220

TFRC/ALB/SLC2A1/NOX4/HSPB1/TF/TNFAIP3

seven

-d enter the gene file for GO enrichment analysis. The file column must contain "ID" (gene ID) and "logFC" (multiple of difference). If there is no multiple of difference, the column "logFC" will be added and the multiple of difference will be set to 0:

IDFDRPValue

LogFC

Regulate

MT1G

2.24E-12

8.09E-15

-4.156082

Down

PLIN4

6.05E-12

2.55E-14

-3.419216

Down

RRM2

6.55E-09

6.50E-11

2.694453

Up

-- no_logFC

If there is a multiple of difference in the input file, you do not need to set it. If not, you need to set this parameter.

-gene 5-GO 4

-- gene sets at least the number of GO term corresponding to each gene. If the number of GO term corresponding to the gene does not reach the set value, then the gene will not be displayed in the figure.

-- GO sets at least the number of gene contained in each GO term. If the number of gene contained in GO term does not reach the set value, then the GO term will not be displayed in the figure.

-z 5-S 0.25-s 0.02

-z sets the font size of the gene ID in the figure,-S sets the interval between the gene in the diagram, and-s sets the interval between the GO term in the diagram.

Use example: $Rscript $scriptdir/GOChord_plot.r-g GO/TP_vs_NT_GO_enrichment_stat.tsv\-d. / 03.deg/fer_deg_gene.tsv-- gene 5-- GO 4 on "R language how to draw GO string diagram" content is introduced here, thank you for reading. If you want to know more about the industry, you can follow the industry information channel. The editor will update different knowledge points for you every day.

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