jiabowang/GAPIT

Error in layout.matrix(mat = layout.matrix, heights = c(100, 80, 120), :

HaoWenhy opened this issue · 4 comments

HaoWenhy commented

Hello,i an sorry to bother you.I have 9 phenotypes data during GAPIT for GWAS analysis.But during the process of performing the analysis,it should just associate the phenotypes of the first PH and the encounter the error reported as below.May l went to ask what could be the cause of this.Thank you !

Error in layout.matrix(mat = layout.matrix, heights = c(100, 80, 120), :
缺少参数"p",也没有缺省值
此外: There were 17 warnings (use warnings() to see them)

jiabowang commented

I have no idea about this error, I do not get any error similar to this one.
Please make sure all pdf files have been closed.
Please send your data to me, so I can help to figure out the reason.

Pascalinesalvado commented

Hello, did you solve this issue because I have the same problem?
Thank you.
Pascaline.

320222102 commented

您好，请问怎么解决呢

guorongdi commented

您好，请问这个问题现在有解决方案吗，我也遇到了相同的问题

library(data.table)
source("~/GuoRongDi_Data/gapit_functions_20240510.txt")
myGD <- fread("./new_mdp_numeric.txt",header=T)
nyGD <- as.data.frame(myGD)
myGM <- fread("mdp_SNP_information.txt",head=T)
myGM = as.data.frame(myGM)
myY <- fread("new_mdp_traits.txt",head=T)
myY <- as.data.frame(myY)
library(GAPIT)
myGAPIT_MLM <- GAPIT(

  • Y=myY,#Phenotype
  • GD=myGD,#Genotype
  • GM=myGM,#Map information
  • PCA.total=3,model="BLINK")
    [1] "--------------------- Welcome to GAPIT ----------------------------"
    [1] "BLINK"
    [1] "--------------------Processing traits----------------------------------"
    [1] "Phenotype provided!"
    [1] "The 1 model in all."
    [1] "BLINK"
    [1] "GAPIT.DP in process..."
    [1] "GAPIT will filter marker with MAF setting !!"
    [1] "The markers will be filtered by SNP.MAF: 0"
    maf_index
    TRUE
    885134
    [1] "Calculating kinship..."
    [1] "Number of individuals and SNPs are 438 and 885134"
    [1] "Kinship created!"
    [1] "Calling prcomp..."
    [1] "Creating PCA graphs..."
    [1] "Joining taxa..."
    [1] "Exporting PCs..."
    [1] "PC created"
    [1] "Filting marker for GAPIT.Genotype.View function ..."
    Error in layout.matrix(mat = layout.matrix, heights = c(100, 80, 120), :
    argument "p" is missing, with no default