Post date: Feb 10, 2020 1:41:46 PM
Tasks done today:
- read one paper (Gill et al 1995)
- started Lewontin Award
Pando data analysis:
Goal of the day: map Pando-identified trees based on PC1 scores
Attention - to mention to Zach -
I used the genotype assigned by 1/1, ect. on the assumption that the previous filter inly kept real hets- is that correct?
I coded hets with 1s, homs with 0s.
I had issues having NAs in the data (for individuals with no genotype assigned e.g. ./. or ./1) thus I transformed NAs into a number, NAs are coded with 2s - is that ok?
Got sidetracked - there was some trees with the same ID number because I hadn't taken into account the -rep or -Rp that was after the number. Now, every tree has a distinct ID number, however, there are some replicates - count the number of points on the map
These indivudals are not found in the set of coordinates using intersect in R
"037-B-rep" "037-B-Rp" "055-S-rep" "129-S-rep" "129-S-Rp" "207-S"
cd /uufs/chpc.utah.edu/common/home/gompert-group1/data/aspen/gbs_pando_plus/Variants_mem_bcftools/rozenn
Add scale and north arrow: http://oswaldosantos.github.io/ggsn/
Need GDAL - asked Zach how to get an update.
Petit pbm : B ans S se superposent - comment les différencier
Graphs presenting the PCA of all trees sequenced for Pando:
- basic PCA plots to have an idea of the data
- first maps of PC1 (not much pattern visible bc very low variance explained by PC1)