Data for the plot_pxg()

[Saikat Bandyopadhyay]

I am trying to extract the data that is being plotted by the plot_pxg() to crate the plot with ggplot instead of the R base.

What is the best way to go about this?

So far I have a function like this but its incomplete:

```

plot_pxg_ggplot <- function(pheno_name, loci){
  # get the peak data related to the loci
  loci_pheno_peak <- qtl_peak_loci %>% filter(
    lodcolumn==pheno_name & manual_annotation_locus== loci)
  # get the loci related marker data
  loci_data <- loci_marker_data[[loci]]
  # convert the data into long format
  loci_data_long <- loci_data %>%
    pivot_longer(
      4:(ncol(loci_data)-1),
      names_to ="lodcolumn",
      values_to = "LOD") %>%
    filter(lodcolumn == pheno_name)

  # get the chromosome where the loci is located
  chr <- unique(loci_data_long$chr)
  # pheno data for the specified phenotype
  pheno_data  <- as.numeric(pheno[,pheno_name])
  pheno_data_inverse_normal <- inverse_normal_transform(pheno_data)
  names(pheno_data_inverse_normal) <- rownames(cross_basic$pheno)
  # subset the allele probability data to only include the markers in the loci

  # get the genotypes for the specified
  genotype <- maxmarg(
    probs = pr,
    map = cross_basic$pmap,
    chr = chr,
    pos = loci_pheno_peak$pos
    )

  geno <- factor(genotype)
  return(geno)

}

```

Thank you.

[Karl Broman]

I'd recommend using the ggplot_pxg function in the qtl2ggplot package.

(Brian Yandell's companion package that implements all of the plotting functions but with ggplot rather than base graphics.)

karl

[Saikat Bandyopadhyay]

Dear Dr Karl, 

I am afraid the ggplot_pxg does not provide the level of customizability I was hoping for and it seems the ggplot_pxg function clusters more individuals in the 'NA' genotype, which is not the case when I use plot_pxg. 

Is there a way, to extract the data as a data frame that I can plot myself?

Thank you so much

[Karl Broman]

I don't quite understand what you're looking for, as the input to these functions (plot_pxg and ggplot_pxg) are a vector of genotypes and a vector of phenotype values, which is presumably the data that you want, for making your own plot.

karl

[Saikat Bandyopadhyay]

Hi Dr Karl,

I figured it out.

I was looking to create a data frame where one of the columns is the genotype and the rest are phenotypes. I was not using the option return_char = TRUE in the maxmarg(), which is why I got confused. But I have the required data structure now.

Thank you very much for your responses, and I am sorry for the error on my part.

Best,

Saikat