Dear Mollinari,
Thanks for your developing excellent software in polyploid genetics. I'm trying to build a genetic map of sweet potato using mappoly2 latest, and after using rf_filter(px.f1.all, thresh.LOD.ph = 5, thresh.LOD.rf = 5, thresh.rf = 0.15, probs = c(0.05, 0.9)), then running group(x = px.f1.all, expected.groups = 5, comp.mat = TRUE, inter = TRUE, LODweight = TRUE)", returns "Error in hclust(as.dist(MSNP), method = "ward.D2", members = apply(Mlod, : invalid length of members", is this an unknown bug and is there any suggestion to solve it?
Bestly,
Jun Zhang

I constructed a map using BExMG and SWxBE and trying to integrate the two... in the calc_consensus_haplo() if i set ncpus=2 then it says, "Error in get(name, envir = envir) : object 'pedigree' not found"

ncpus=1 works fine.

thanks

Jeekin

When plotting a single RF matrix its is labeled as Lg1 and for multiple Lg as in this example lg=c(1,10,3,24) it labels 1:4

Using vignette data or my own raises the following:

> ## testing plot_map
> download.file("https://github.com/mmollina/mappoly2_vignettes/raw/main/I195_x_F1-85-209_map.rda", 
+              destfile = "temp_file.rda")
trying URL 'https://github.com/mmollina/mappoly2_vignettes/raw/main/I195_x_F1-85-209_map.rda'
Content type 'application/octet-stream' length 11822960 bytes (11.3 MB)
==================================================
downloaded 11.3 MB

> load("temp_file.rda")
> ## testing plot_map
> library(mappoly2)
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'. 
> load("temp_file.rda")
> ls()
[1] "I195xF1_85_209_map"
> # just build first lg
> I195xF1_85_209_map <- mapping(I195xF1_85_209_map,
+                               lg = 1,
+                               type = "genome", 
+                               error = 0.05, ncpus = 4)
Multi-locus map estimation
Processing linkage group
   Conf. 1 :..............................
            ..............................
            ................
Done with map estimation
> plot_map(I195xF1_85_209_map,type = 'genome')
Error: assert_that: missing values present in assertion

Hi @mmollina
Since I prefer to organise complex workflows like mapping in targets pipelines, I am interested to discuss what would be the best ways to work with mappoly2 objects and workflows.
It was very difficult to do this in mappoly due to references to external objects.

• Are all the mappoly2 objects self-contained, and thus suitable for being persisted as targets objects?
• What should we consider in terms of the functional style of mappoly2? More specifically Im trying to understand the idiom that you use use of sequential updates to an object as below. Im assuming that each of these calls is updating a specific slot, and that we want to avoid copying a large object?

#> Multi-locus map estimation

s <- mapping(s, type = "mds", parent = "p1", ncpus = ncores)
s <- mapping(s, type = "genome", parent = "p1", ncpus = ncores)
s <- mapping(s, type = "mds", parent = "p2", ncpus = ncores)
s <- mapping(s, type = "genome", parent = "p2", ncpus = ncores)