Leishmania strain visualizations: 2020-02-25

1 Comparing Leishmania strain mapping

1.1 Leishmania amazonensis reference

6 mappings against L. amazonensis.

Panamensis and major map terribly against amazonensis. It would appear that one of our braziliensis strains is actually amazonensis. I say this because the second braziliensis mapping shows constituitively more differences than the first.

1.2 Leishmania braziliensis 2903 reference

6 mappings against L. braziliensis 2903.

This was a surprise to me. Leishmania braziliensis 2903 is much more similar to L. panamensis than it is to anything else.

1.3 Leishmania braziliensis 2904 reference

6 mappings against L. braziliensis 2904.

I previously thought that 2903 was relatively different than 2904. This was incorrect.

pander::pander(sessionInfo())
message(paste0("This is hpgltools commit: ", get_git_commit()))
this_save <- paste0(gsub(pattern="\\.Rmd", replace="", x=rmd_file), "-v", ver, ".rda.xz")
message(paste0("Saving to ", this_save))
tmp <- sm(saveme(filename=this_save))