Updated test

src/BigRiverQTL.jl

@@ -2,7 +2,6 @@ module BigRiverQTL
     using BulkLMM
     using DataFrames, JSON, CSV
     using Statistics
-    using Distributed
     using LinearAlgebra
     import StatsBase: sample
 

src/plots/plots_eqtl.jl

@@ -12,7 +12,7 @@ Generates a scatter plot for eQTL analysis.
 - `threshold` is the LOD threshold value, default is `5.0``.
 
 """
-function plot_eQTL(multiLODs::Array{Float64, 2}, dfpInfo::DataFrame, dfgInfo::DataFrame;
+function plot_eQTL(multiLODs::Array{Float64, 2}, dfpInfo::Pmap, dfgInfo::Gmap;
                    kwargs...)
 
                    return plot_eQTL(multiLODs,pmap2df(dfpInfo), gmap2df(dfgInfo); kwargs...)

test/data/BXD/ReadMe.md

@@ -0,0 +1,27 @@
+## BXD mouse recombinant inbred lines
+
+Genotype and phenotype data for the mouse BXD recombinant inbred
+lines, from [GeneNetwork](http://gn2.genenetwork.org).
+
+### File format
+
+See the [R/qtl2 input file format](https://kbroman.org/qtl2/assets/vignettes/input_files.html).
+
+
+
+### Citation
+
+Need to add a citation.
+
+
+
+### Use with [R/qtl2](https://kbroman.org/qtl2)
+
+Load these data into R directly from the web as follows:
+
+```r
+library(qtl2)
+file <- paste0("https://raw.githubusercontent.com/rqtl/",
+               "qtl2data/main/BXD/bxd.zip")
+bxd <- read_cross2(file)
+```

test/data/BXD/bxd.json

@@ -0,0 +1,23 @@
+{
+  "description": "BXD mouse data from GeneNetwork",
+  "crosstype": "risib",
+  "sep": ",",
+  "na.strings": ["-", "NA"],
+  "comment.char": "#",
+  "geno": "bxd_geno.csv",
+  "gmap": "bxd_gmap.csv",
+  "pmap": "bxd_pmap.csv",
+  "pheno": "bxd_pheno.csv",
+  "phenocovar": "bxd_phenocovar.csv",
+  "alleles": ["B", "D"],
+  "x_chr": "X",
+  "genotypes": {
+    "B": 1,
+    "D": 2
+  },
+  "geno_transposed": true,
+  "cross_info": {
+    "file": "bxd_crossinfo.csv",
+    "BxD": 0
+  }
+}

test/data/BXD/bxd_crossinfo.csv

@@ -0,0 +1,203 @@
+# Cross info for BXD data
+#(all lines formed from cross between female B and male D)
+# nrow 198
+# ncol 2
+id,cross_direction
+BXD1,BxD
+BXD2,BxD
+BXD5,BxD
+BXD6,BxD
+BXD8,BxD
+BXD9,BxD
+BXD11,BxD
+BXD12,BxD
+BXD13,BxD
+BXD14,BxD
+BXD15,BxD
+BXD16,BxD
+BXD18,BxD
+BXD19,BxD
+BXD20,BxD
+BXD21,BxD
+BXD22,BxD
+BXD23,BxD
+BXD24,BxD
+BXD24a,BxD
+BXD25,BxD
+BXD27,BxD
+BXD28,BxD
+BXD29,BxD
+BXD30,BxD
+BXD31,BxD
+BXD32,BxD
+BXD33,BxD
+BXD34,BxD
+BXD35,BxD
+BXD36,BxD
+BXD37,BxD
+BXD38,BxD
+BXD39,BxD
+BXD40,BxD
+BXD41,BxD
+BXD42,BxD
+BXD43,BxD
+BXD44,BxD
+BXD45,BxD
+BXD48,BxD
+BXD48a,BxD
+BXD49,BxD
+BXD50,BxD
+BXD51,BxD
+BXD52,BxD
+BXD53,BxD
+BXD54,BxD
+BXD55,BxD
+BXD56,BxD
+BXD59,BxD
+BXD60,BxD
+BXD61,BxD
+BXD62,BxD
+BXD63,BxD
+BXD64,BxD
+BXD65,BxD
+BXD65a,BxD
+BXD65b,BxD
+BXD66,BxD
+BXD67,BxD
+BXD68,BxD
+BXD69,BxD
+BXD70,BxD
+BXD71,BxD
+BXD72,BxD
+BXD73,BxD
+BXD73a,BxD
+BXD73b,BxD
+BXD74,BxD
+BXD75,BxD
+BXD76,BxD
+BXD77,BxD
+BXD78,BxD
+BXD79,BxD
+BXD81,BxD
+BXD83,BxD
+BXD84,BxD
+BXD85,BxD
+BXD86,BxD
+BXD87,BxD
+BXD88,BxD
+BXD89,BxD
+BXD90,BxD
+BXD91,BxD
+BXD93,BxD
+BXD94,BxD
+BXD95,BxD
+BXD98,BxD
+BXD99,BxD
+BXD100,BxD
+BXD101,BxD
+BXD102,BxD
+BXD104,BxD
+BXD105,BxD
+BXD106,BxD
+BXD107,BxD
+BXD108,BxD
+BXD109,BxD
+BXD110,BxD
+BXD111,BxD
+BXD112,BxD
+BXD113,BxD
+BXD114,BxD
+BXD115,BxD
+BXD116,BxD
+BXD117,BxD
+BXD119,BxD
+BXD120,BxD
+BXD121,BxD
+BXD122,BxD
+BXD123,BxD
+BXD124,BxD
+BXD125,BxD
+BXD126,BxD
+BXD127,BxD
+BXD128,BxD
+BXD128a,BxD
+BXD130,BxD
+BXD131,BxD
+BXD132,BxD
+BXD133,BxD
+BXD134,BxD
+BXD135,BxD
+BXD136,BxD
+BXD137,BxD
+BXD138,BxD
+BXD139,BxD
+BXD141,BxD
+BXD142,BxD
+BXD144,BxD
+BXD145,BxD
+BXD146,BxD
+BXD147,BxD
+BXD148,BxD
+BXD149,BxD
+BXD150,BxD
+BXD151,BxD
+BXD152,BxD
+BXD153,BxD
+BXD154,BxD
+BXD155,BxD
+BXD156,BxD
+BXD157,BxD
+BXD160,BxD
+BXD161,BxD
+BXD162,BxD
+BXD165,BxD
+BXD168,BxD
+BXD169,BxD
+BXD170,BxD
+BXD171,BxD
+BXD172,BxD
+BXD173,BxD
+BXD174,BxD
+BXD175,BxD
+BXD176,BxD
+BXD177,BxD
+BXD178,BxD
+BXD180,BxD
+BXD181,BxD
+BXD183,BxD
+BXD184,BxD
+BXD186,BxD
+BXD187,BxD
+BXD188,BxD
+BXD189,BxD
+BXD190,BxD
+BXD191,BxD
+BXD192,BxD
+BXD193,BxD
+BXD194,BxD
+BXD195,BxD
+BXD196,BxD
+BXD197,BxD
+BXD198,BxD
+BXD199,BxD
+BXD200,BxD
+BXD201,BxD
+BXD202,BxD
+BXD203,BxD
+BXD204,BxD
+BXD205,BxD
+BXD206,BxD
+BXD207,BxD
+BXD208,BxD
+BXD209,BxD
+BXD210,BxD
+BXD211,BxD
+BXD212,BxD
+BXD213,BxD
+BXD214,BxD
+BXD215,BxD
+BXD216,BxD
+BXD217,BxD
+BXD218,BxD
+BXD219,BxD
+BXD220,BxD