LDdecayPlotTool

LDdecayPlotTool鸣谢/Acknowledgement引用/Citation最新更新/Updates功能/features生成图展示/Showing the plot of examples均值图像/the average LD Decay plot across all chromosome分染色体图像（显示r^2）/the LD plot with a r^2^ value for each chromosome.分染色体图像（不显示r^2）/the chromosomes plot without a r^2^ value生成表展示/Showing the example of tables使用方法/How to use it讨论/Help&Bugs

制作：张敖 https://datahold.cn Code by Ao Zhang https://datahold.cn

鸣谢/Acknowledgement

张学才，CIMMYT，指导 Xuecai Zhang, CIMMYT, guide

曹士亮，黑龙江农科院，测试玉米基因组 Shiliang Cao, Heilongjiang Academy of Agricultural Sciences, testing maize genome

袁一冰，四川省农科院，测试玉米基因组 Yibing Yuan, Sichuan Academy of Agricultural Sciences, testing maize genome

宋俊乔，安阳市农科院，测试玉米基因组 Junqiao song, Anyang Academy of Agricultural Sciences, testing maize genome

冉虎，印度农业研究院，测试小麦基因组 Rahul, India Agricultrual Research Institute, testing wheat genome

陈珊，沈阳农业大学，译成英文 Shan Chen, Shenyang Agruicultural University, translate into English

瞿静涛，上海农科院，测试特种玉米基因组 Jingtao Qu, Shanghai Academy of Agricultural Sciences, testing waxy maize and sweet m;aize genomes

引用/Citation

Linkage disequilibrium analysis was performed using TASSEL software and then the visualization of LD decay was ploted by the R programing integrated script provided by Zhang et al (2022).

Zhang, A., Chen, S., Cui, Z. et al. Genomic prediction of drought tolerance during seedling stage in maize using low-cost molecular markers. Euphytica 218, 154 (2022). https://doi.org/10.1007/s10681-022-03103-y

功能/features

直接利用TASSEL的LD分析生成的文件。 The LD decay plot can be drawn directly using the files generated by the LD analysis of TASSEL.
生成整体的LD衰减图（自行保存为PDF、TIFF、JPG、PNG等格式）。 Generate the overall LD decay map (can be saved as PDF, TIFF, JPG, PNG, etc.).
生成每条染色体及总体均值的LD衰减图（可自行保存为PDF、TIFF、JPG、PNG等格式）。 Generate the LD decay map of each chromosome and the overall mean (can be saved as PDF, TIFF, JPG, PNG, etc.)
生成可供Excel画图的表格（文件名：群体名称+LD Decay Plot .csv）。
Generate a table for Excel to plot (file name: population name + LD Decay Plot .csv).
快速读取大文件，1.4G文件1min内读取完毕。 Quickly read large files, a 1.4G file can be improve within 1min.
根据简单线性模型，估算比较精确的LD衰减值。 Using Simple Linear Equation to calculate the LD decay value.

生成图展示/Showing the plot of examples

均值图像/the average LD Decay plot across all chromosome

DTMA LD Decay Plot

分染色体图像（显示r^2）/the LD plot with a r^2^ value for each chromosome.

DTMA LD Decay Plot chr

分染色体图像（不显示r^2）/the chromosomes plot without a r^2^ value

DTMA LD Decay Plot chr without r2

生成表展示/Showing the example of tables

Scale Distance (kb)	Chr1	Chr2	Chr3	Chr4	Chr5	Chr6	Chr7	Chr8	Chr9	Chr10	Mean
0	1	1	1	1	1	1	1	1	1	1	1
0.5	0.36	0.35	0.35	0.38	0.36	0.35	0.34	0.36	0.36	0.36	0.36
1	0.16	0.14	0.15	0.15	0.14	0.14	0.14	0.16	0.15	0.16	0.15
2	0.13	0.11	0.12	0.13	0.12	0.11	0.11	0.13	0.12	0.13	0.12
5	0.11	0.1	0.1	0.1	0.09	0.09	0.09	0.11	0.1	0.1	0.1
10	0.08	0.07	0.07	0.08	0.07	0.07	0.07	0.08	0.08	0.08	0.08
20	0.07	0.06	0.07	0.06	0.06	0.06	0.06	0.08	0.06	0.07	0.06
30	0.07	0.05	0.06	0.06	0.05	0.06	0.06	0.06	0.05	0.06	0.06
50	0.06	0.05	0.06	0.06	0.05	0.05	0.05	0.06	0.06	0.06	0.06

Chromosome	LD Decay Distance (kb)
Chr1	6.28
Chr2	4.55
Chr3	5.73
Chr4	5.12
Chr5	4.17
Chr6	3.74
Chr7	3.54
Chr8	6.62
Chr9	4.55
Chr10	4.91
Mean	4.91

使用方法/How to use it

推荐将所有文件（包括r文件和LD衰减文件）放在同一个目录下，然后在R Studio中运行下列代码。 Please put all the files in the same folder. Then run the following code in the Rstudio software.

海外： Overseas:


rm(list=ls())   # Clear the Environment Variables
coordinateScale <- c(0, 500, 1000, 2000, 5000, 10000, 20000, 30000, 50000)   # x coordinate axis, unit is bp
unit <- "Kb"   # Units on the image: "Kb" or "bp"
pop.name <- "DTMA"    # The population's name 
plotTitle <- "LD Decay Plot"   # The title of plot  
lineWidth <- 2   # the width of line  
lineColor <- "blue"   # The color of line 
#lineColor <- "blue","brown","green","gray","gold","darkblue","lightblue","red","orange","tan","yellowgreen")   # The color of line 
dot <- "o"   # "o" is true, "l" is false 
dottedLine <- TRUE # TRUE or FALSE 
dividingLine <- c(0.1)   # 0.1 or 0.2 or c(0.1,0.2)
plotChrR2 <- TRUE   # R^2 value display, TRUE represents yes, and F means no.
source("https://aozhangchina.github.io/R/LDdecay/LDdecayV4.r",encoding = "utf-8")   # the internet is required.

国内： China:


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rm(list=ls())   # Clear the Environment Variables 清空环境变量 
coordinateScale <- c(0, 500, 1000, 2000, 5000, 10000, 20000, 30000, 50000)   # x coordinate axis, unit is bp 坐标x轴,按照pb填写
unit <- "Kb"   # Units on the image: "Kb" or "bp" 图像单位
pop.name <- "DTMA"    # The population's name 群体名称
plotTitle <- "LD Decay Plot"   # The title of plot  图表标题
lineWidth <- 2   # the width of line  线宽
lineColor <- "blue"   # The color of line 线颜色
#lineColor <- "blue","brown","green","gray","gold","darkblue","lightblue","red","orange","tan","yellowgreen")   # The color of line 线颜色
dot <- "o"   # "o" is true, "l" is false 线型："l"是折线，"o"是带点的折线
dottedLine <- TRUE # TRUE or FALSE 
dividingLine <- c(0.1)   # 0.1 or 0.2 or c(0.1,0.2)
plotChrR2 <- TRUE   # R^2 value display 全染色体图例中是否显示r^2值，TURE：显示，FLASE：不显示
source("https://dataholdcn.cn/R/LDdecay/LDdecayV4.r",encoding = "utf-8")   # 加载程序文件，需要联网

然后选择LD数据文件，如：allLD.csv。 Choose a LD file, like [allLD.csv].
程序自动运行直至全部完毕。 Please wait for the program to complete running automatically.
最后一行会显示估算的比较精确的LD衰减值，并显示两个图像。 The last line of console will give you a reference value of LD decay. You can also get plots.

讨论/Help&Bugs

用户请提交Bug或使用中有任何问题，请在lecent.wang上讨论，我们定期查看。

Users please to reply this post (lecent.wang) to discuss any questions about the linkage disequilibrium decay and plot.