How to use maf_oncoplot.r in R language
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maf_oncoplot.r Mutation Comment File Classification Visualization maftools
Usage:Rscript /share/nas1/zhangll/MAF/code/maf_oncoplot.r -usage: /share/nas1/zhangll/MAF/code/maf_oncoplot.r [-h] -i maffle-m metadata -g group [-a additive [additive ...]] [-T topgene] [-l genelist [genelist ...]] [-t] [-o outdir] [-H height] [-W width]Mutation annotation file classificationvisualization:https://www.. com/article/1518optional arguments: -h, --help show this help message and exit -i maffile, --maf maffile input the maf file[required] -m metadata, --meta metadata input metadata file path[required] -g group, --group group input group id in metadata file to classification visualization[required] -a additive [additive ...], --additive additive [additive ...] add additional class[optional,default: NULL] -T topgene, --top topgene Number of top genes displayed [optional, default: 20] -l genelist [genelist ...], --genelist genelist [genelist ...] the selected gene list to display [optional, default: NULL] -t, --showtitle whether show maftools title of plot [optional, default: False] -o outdir, --outdir outdir output file directory [default cwd] -H height, --height height the height of pic inches [default 8] -W width, --width width the width of pic inches [default 8] Parameter description:
-i Path to mutation annotation file maf, which can be downloaded directly from TCGA database:
Hugo_Symbol
Entrez_Gene_Id
Center
NCBI_Build
Chromosome
Start_Position
End_Position
Strand
Variant_Classification
MFN2
9927
WUGSC
GRCh48
chr1
1200177712001777
+
Missense_Mutation
KCNG3
170850
WUGSC
GRCh48
chr2
4244457842444578
+Missense_Mutation
MAP2
4133WUGSCGRCh48
chr2
209692762
209692762
+
Missense_Mutation
HEG1
57493
WUGSC
GRCh48
chr3
125010546
125010546
+
Missense_Mutation
PCDHB11
56125
WUGSC
GRCh48
chr5
141200541141200541
+
Missense_Mutation
NSD1
64324
WUGSC
GRCh48
chr5
177294257177294257
+
Missense_Mutation
F13A1
2162WUGSCGRCh48
chr6
61746096174609
+
Missense_Mutation
PRRT4
401399
WUGSCGRCh48
chr7
128359624128359624
+
Missense_Mutation
FBP2
8789
WUGSCGRCh48
chr9
94558941
94558941
+
Missense_Mutation
-m metadata file, all kinds of characteristic information of patient sample, must contain the column of patient TCGA number named by patient:
patient
sample
shortLetterCode
tumor_stagetissue_or_organ_of_origin
alcohol_history
gender
ethnicity
race
TCGA-M9-A5M8
TCGA-M9-A5M8-01A
TP
stage iia
Lower third of esophagus
Yes
male
not reported
not reported
TCGA-R6-A6DQ
TCGA-R6-A6DQ-01B
TP
not reported
Lower third of esophagus
Yes
female
not hispanic or latino
white
TCGA-LN-A9FP
TCGA-LN-A9FP-01A
TP
stage iiaMiddle third of esophagus
Yes
female
not hispanic or latino
asian
TCGA-LN-A4MQ
TCGA-LN-A4MQ-01A
TP
stage iii
Lower third of esophagus
No
male
not hispanic or latino
asian
TCGA-JY-A93D
TCGA-JY-A93D-01A
TP
stage iiic
Lower third of esophagus
Yes
male
not reported
white
TCGA-IG-A3YB
TCGA-IG-A3YB-01A
TP
stage iiia
Lower third of esophagus
No
male
not hispanic or latino
white
TCGA-IC-A6RF
TCGA-IC-A6RF-01A
TP
stage ia
Middle third of esophagus
Yes
female
not hispanic or latino
white
TCGA-VR-A8EX
TCGA-VR-A8EX-01A
TP
stage iva
Middle third of esophagus
No
male
not reported
not reported
-g Specifies the metadata group column name. If the group name has spaces, it should be enclosed in quotation marks.
-a Additional grouping column names, the results will be shown in the figure
-T Specifies the number of top genes to be displayed, default 20
-l Specify the list of genes to be displayed, separated by spaces, default NULL
Examples of use: Rscript /share/nas1/zhangll/MAF/code/maf_oncoplot.r -i /share/nas1/zhangll/MAF/TCGA-ESCA.maf_maftools.maf -m /share/nas1/huangls/project/TCGA_ESCA/metadata.tsv -g gender"How to use maf_oncoplot.r in R language" is introduced here. Thank you for reading it. If you want to know more about industry-related knowledge, you can pay attention to the website. Xiaobian will output more high-quality practical articles for everyone!
