参考学习资料：https://github.com/cgrace1978/manhplot/
MANHATTAN++ is software to generate a transposed manhattan heatmap, implemented in R.
Getting Started
You need to install the latest version of R The R package can be run on Windows and Linux, you must specify paths to the filenames you are using as input and output.
To install the software from the GIT repository:
install.packages("devtools")
library(devtools)
install_github("cgrace1978/manhplot", dependencies = T, force = T)
The following command will run the plot with default data in the package. The pdf (test.pdf) will be created in the current working directory in R (This can be viewed using the getwd() command):
library(manhplot)
infile<-system.file("extdata","cad.add.160614_manhformat.txt.gz",package = "manhplot")
configfile<-system.file("extdata","config.txt", package = "manhplot")
snpfile<-system.file("extdata","56cad.add.160614.variants.txt", package = "manhplot")
## Run manhattan++ with the default paramaters and files included in the package
manhplusplot(infile = infile,outfile = "test", configfile = configfile, snpfile = snpfile)
For more information on using manhattan++ please visit the Manhattan++ wiki
Citation
To use Manhattan++ please cite the following paper:
Grace et al
Manhattan++: displaying genome-wide association summary statistics with multiple annotation layers
BMC Bioinformatics 2019; 20(1):610
PubMed: 31775616
运行结果如下：
> infile
[1] "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/manhplot/extdata/cad.add.160614_manhformat.txt.gz"
> configfile
[1] "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/manhplot/extdata/config.txt"
> snpfile
[1] "/Library/Frameworks/R.framework/Versions/3.6/Resources/library/manhplot/extdata/56cad.add.160614.variants.txt"
在终端中显示为：
(base) Cheng-MacBook-Pro:~ chelsea$ cd /Library/Frameworks/R.framework/Versions/3.6/Resources/library/manhplot/extdata/
(base) Cheng-MacBook-Pro:extdata chelsea$ ll
total 2256
-rw-rw-r-- 1 chelsea admin 3394 Feb 17 09:58 56cad.add.160614.variants.txt
-rw-rw-r-- 1 chelsea admin 1145757 Feb 17 09:58 cad.add.160614_manhformat.txt.gz
-rw-rw-r-- 1 chelsea admin 1191 Feb 17 09:58 config.txt
(base) Cheng-MacBook-Pro:extdata chelsea$ head 56cad.add.160614.variants.txt
markername gene chr pos eaf OR Pvalue novel
rs11206510 PCSK9 1 55496039 0.847627 1.08 2.34E-0FALSE
rs9970807 PPAP2B 1 56965664 0.915097 1.13 5E-14 FALSE
rs7528419 SORT1 1 109817192 0.78582 1.12 1.97E-23 FALSE
rs6689306 IL6R 1 154395946 0.447545 1.06 2.6E-09FALSE
rs67180937 MIA3 1 222823743 0.663052 1.08 1.01E-1FALSE
rs16986953 AK097927 2 19942473 0.104706 1.09 1.45E-08 FALSE
2:21378433:D APOB 2 21378433 0.745655 1.07 2.89E-0FALSE
2:44074126:D ABCG5-ABCG8 2 44074126 0.744839 1.06 0.000000026 FALSE
rs7568458 VAMP5-VAMP8-GGCX 2 85788175 0.448518 1.06 3.62E-10 FALSE
(base) Cheng-MacBook-Pro:extdata chelsea$ zless -S cad.add.160614_manhformat.txt.gz |head
chr pos pvalue maf conseq
1 921716 .0016563 .499 0
1 924528 .009725 .543 0
1 930751 .0014219 .349 0
1 931362 .001282 .354 0
1 933790 .0066479 .552 0
1 935222 .0038324 .546 0
1 940005 .0012462 .377 0
1 941284 .0024818 .355 0
1 941334 .001352 .354 0
(base) Cheng-MacBook-Pro:extdata chelsea$ head config.txt
#### CONFIG file for use with MANH++ - Do not modify the first 10 lines
## min.count: The lower cell count threshold to accept this config
## max.count: The upper cell count threshold to accept this config
## maf: Is MAF detection active for this config - is there any variants within a cell with MAF < threshold?
## conseq: Is HIGH impact consequence active? Are there any variants with HIGH impact consequence in the cell?
## col: The colour which cells for this config
## idx: the index to use for this cell in the heatmap - MUST BE CONSECUTIVE FROM START TO END - STARTING AT 1
"## type: val - an config entry, oddchr - the odd chromosome, evenchr - the even chromosome"
## report: Are these annotations labeled on the heatmap
#####
曼哈顿图展示如下：
看上去比较高级
具体参数解析见原文https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3201-y
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