Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Computation of genetic diversity stats and comparison between populations #43

Open
wants to merge 32 commits into
base: master
Choose a base branch
from
Open

Computation of genetic diversity stats and comparison between populations #43

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
32 commits
Select commit Hold shift + click to select a range
1851dcd
Initial port of LH work
Oct 8, 2020
51bb899
WIP using PCA to identify colors
Oct 8, 2020
4a9f25f
Merge branch 'master' into q13-design-pca-figure
Oct 9, 2020
7b25d97
Merge branch 'master' of https://github.com/malariagen/ag1000g-phase3…
Oct 9, 2020
8f5a71e
WIP with colours + bokeh
Oct 9, 2020
af6a11d
Updated with population definitions for WWA
Oct 13, 2020
8977c3c
a notebook for comparison of Watterson s theta at various samples siz…
jonbrenas Oct 15, 2020
0dcc223
Add population definitions
Oct 19, 2020
8ce548a
Finalize gamb_colu populations
Oct 20, 2020
f27225d
Merge branch 'master' of https://github.com/malariagen/ag1000g-phase3…
Oct 20, 2020
2950c4b
Complete gamb_colu figure and edits to ag3.py
Oct 20, 2020
6f3e0a4
Remove old code, tidy, add svg
Oct 20, 2020
3a70f04
Change population > location for clarity
Oct 21, 2020
96ccfc0
minor edits following AM discussion
Oct 21, 2020
cda1f78
updates
Oct 26, 2020
322bbf6
complete merge re ag3.py
Oct 26, 2020
e3f6462
update approach
Oct 28, 2020
cc27099
removing notes committed in error
Oct 28, 2020
7316eb2
WIP: PoC calc location colours w/ CIELAB colour space
leehart Oct 30, 2020
28c2f93
Merge remote-tracking branch 'origin/LH_recalc_location_colours' into…
Nov 2, 2020
5320129
Moved the zarr files to the cloud and started to reorganize the noteb…
jonbrenas Nov 2, 2020
6c39e4b
Update with LH new colours
Nov 3, 2020
4fe91bf
Checked that arabiensis were significantly different from gambiae as …
jonbrenas Nov 5, 2020
d7ec11e
a notebook for comparison of Watterson s theta at various samples siz…
jonbrenas Oct 15, 2020
9243c8a
Moved the zarr files to the cloud and started to reorganize the noteb…
jonbrenas Nov 2, 2020
d52c618
Checked that arabiensis were significantly different from gambiae as …
jonbrenas Nov 5, 2020
5aa29e0
a notebook for comparison of Watterson s theta at various samples siz…
jonbrenas Oct 15, 2020
6e3e851
Moved the zarr files to the cloud and started to reorganize the noteb…
jonbrenas Nov 2, 2020
557c452
Checked that arabiensis were significantly different from gambiae as …
jonbrenas Nov 5, 2020
dfcdafc
Rebase didn't go as smoothly as I hoped.
jonbrenas Nov 5, 2020
25d03fc
Update on the Watterson's theta front. It has been computed for vario…
jonbrenas Feb 2, 2021
db19845
Here are the notebooks computing Watterson's theta. They may need to …
jonbrenas Feb 15, 2021
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
30,671 changes: 30,671 additions & 0 deletions content/images/pca/gamb_colu.svg
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
2,659 changes: 2,659 additions & 0 deletions content/population_definitions.yml
View file
Open in desktop

Large diffs are not rendered by default.

181 changes: 181 additions & 0 deletions notebooks/Watt-Theta-arab.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,181 @@
dps,mean,population,country,pop_n,species,year
10,0.00948773113388483,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
10,0.009472429640671704,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
10,0.009622223205810706,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
10,0.00941283435131533,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
10,0.009584372143651928,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
15,0.009868894369557466,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
15,0.009868894369557462,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
15,0.009850143181775493,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
15,0.009918657137132695,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
15,0.00980759240950102,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
20,0.010168329831274931,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
20,0.010055482730491856,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
20,0.010169673249141396,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
20,0.010270429589126284,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
20,0.010237515851397887,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
25,0.010380029983538628,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
25,0.010408734054653927,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
25,0.010463590723896497,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
25,0.010373651301068562,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
25,0.010499949213975873,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
30,0.010641978559321686,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
30,0.01065974684639753,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
30,0.010641978559321688,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
30,0.010654845249962814,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
30,0.010570292711463971,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
35,0.010861593534294264,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
35,0.010967730953370511,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
35,0.010843805140035676,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
35,0.010895984429860868,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
35,0.010795776475537486,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
40,0.011031744112531962,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
40,0.011038666353138025,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
40,0.010918103995915732,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
40,0.011015592217784477,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
40,0.01094521610495615,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
45,0.011239931470561512,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
45,0.011251199007497567,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
45,0.011118805448498923,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
45,0.011207818990293756,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
45,0.011162748842549535,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
50,0.011258319724605543,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
50,0.01129143080658566,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
50,0.011281497481991623,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
50,0.01129694932024901,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
50,0.011352134456882535,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
55,0.011516036327746568,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
55,0.0114786501177807,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
55,0.011424467204786693,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
55,0.011484068409080101,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
55,0.011425009033916633,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
60,0.011584664689748716,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
60,0.011496187379488848,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
60,0.01163103532825841,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
60,0.01154095903046372,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
60,0.011512177254837016,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
65,0.011672440725641497,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
65,0.011654061410120644,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
65,0.011689244671260559,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
65,0.011648810177114688,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
65,0.01170499837027843,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
70,0.011786988703061324,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
70,0.011804602099795999,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
70,0.011756942320396289,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
70,0.011762640772281036,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
70,0.011706692335594416,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
75,0.011869558427431703,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
75,0.011867000332943032,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
75,0.011854209860499678,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
75,0.011856767954988351,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
75,0.011832210247897112,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
80,0.011942395934511582,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
80,0.011943407444775803,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
80,0.01194441895504002,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
80,0.011944924710172129,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
80,0.011944924710172129,UGA_2_arabiensis_2012,UGA,2,arabiensis,2012
10,0.00881366009075932,TZA_3_arabiensis_2012,TZA,3,arabiensis,2012
10,0.008904663708290005,TZA_3_arabiensis_2012,TZA,3,arabiensis,2012
10,0.00891835451800701,TZA_3_arabiensis_2012,TZA,3,arabiensis,2012
10,0.008934461352968192,TZA_3_arabiensis_2012,TZA,3,arabiensis,2012
10,0.00892962930247984,TZA_3_arabiensis_2012,TZA,3,arabiensis,2012
15,0.009283280351135901,TZA_3_arabiensis_2012,TZA,3,arabiensis,2012
15,0.009258038367583248,TZA_3_arabiensis_2012,TZA,3,arabiensis,2012
15,0.009390017881587122,TZA_3_arabiensis_2012,TZA,3,arabiensis,2012
15,0.00905754489822217,TZA_3_arabiensis_2012,TZA,3,arabiensis,2012
15,0.00909216247566581,TZA_3_arabiensis_2012,TZA,3,arabiensis,2012
20,0.009228609033682538,TZA_3_arabiensis_2012,TZA,3,arabiensis,2012
20,0.009381086961526336,TZA_3_arabiensis_2012,TZA,3,arabiensis,2012
20,0.00935623373099673,TZA_3_arabiensis_2012,TZA,3,arabiensis,2012
20,0.009512741912439924,TZA_3_arabiensis_2012,TZA,3,arabiensis,2012
20,0.009314587777136311,TZA_3_arabiensis_2012,TZA,3,arabiensis,2012
25,0.00964903297246905,TZA_3_arabiensis_2012,TZA,3,arabiensis,2012
25,0.00955271486717105,TZA_3_arabiensis_2012,TZA,3,arabiensis,2012
25,0.009764487125177248,TZA_3_arabiensis_2012,TZA,3,arabiensis,2012
25,0.00977341728063534,TZA_3_arabiensis_2012,TZA,3,arabiensis,2012
25,0.00952656226904378,TZA_3_arabiensis_2012,TZA,3,arabiensis,2012
30,0.009766430896170632,TZA_3_arabiensis_2012,TZA,3,arabiensis,2012
30,0.0097799102863661,TZA_3_arabiensis_2012,TZA,3,arabiensis,2012
30,0.009806869066757035,TZA_3_arabiensis_2012,TZA,3,arabiensis,2012
30,0.009597325819172945,TZA_3_arabiensis_2012,TZA,3,arabiensis,2012
30,0.009782361084583455,TZA_3_arabiensis_2012,TZA,3,arabiensis,2012
35,0.009925923996292496,TZA_3_arabiensis_2012,TZA,3,arabiensis,2012
35,0.009717206836991723,TZA_3_arabiensis_2012,TZA,3,arabiensis,2012
35,0.009889754261300034,TZA_3_arabiensis_2012,TZA,3,arabiensis,2012
35,0.009844690329178276,TZA_3_arabiensis_2012,TZA,3,arabiensis,2012
35,0.009828680774345547,TZA_3_arabiensis_2012,TZA,3,arabiensis,2012
10,0.009383842048385199,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
10,0.00927753693764139,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
10,0.009285590355121984,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
10,0.009301697190083166,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
10,0.009346796327974477,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
15,0.009714557670121238,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
15,0.009663352503485855,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
15,0.009730424059782906,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
15,0.009770811233467153,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
15,0.009425356658560837,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
20,0.010039361716094274,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
20,0.009897631131182196,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
20,0.009993685508634458,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
20,0.009840535871857427,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
20,0.009939948793975851,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
25,0.010284349746487637,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
25,0.01016889559377944,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
25,0.010265851567324446,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
25,0.010251180597643293,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
25,0.010248629124655266,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
30,0.010439175006835333,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
30,0.010461232190791552,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
30,0.01042079402020515,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
30,0.010450203598813443,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
30,0.010456330594356838,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
35,0.010525392882806937,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
35,0.010649318696141774,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
35,0.010591802888039003,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
35,0.010644575124339481,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
35,0.010595360566890722,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
40,0.010798695345461113,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
40,0.010723127552178238,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
40,0.010691977469450945,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
40,0.010806771292834857,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
40,0.01071389789803682,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
45,0.010891201202390616,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
45,0.010838807155637958,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
45,0.010837117025097551,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
45,0.010846694431493196,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
45,0.010875426650680139,TZA_2_arabiensis_2012,TZA,2,arabiensis,2012
10,0.008890972898573,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
10,0.008909495758778361,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
10,0.009043182488956178,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
10,0.008859564570398692,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
10,0.00891030110052642,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
15,0.009031581715139443,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
15,0.009320782726699842,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
15,0.00971744246824154,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
15,0.009856633977546174,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
15,0.009061872095402625,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
20,0.009811652387728426,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
20,0.0097451532033384,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
20,0.009806278716262565,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
20,0.009819041185993985,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
20,0.009358920566729661,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
25,0.009967329227725351,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
25,0.010011980005015813,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
25,0.009431519900239793,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
25,0.009508701958127594,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
25,0.009995395430593643,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
30,0.010146917319415421,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
30,0.010157333211839191,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
30,0.009637763989759348,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
30,0.00948458910117449,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
30,0.009555049549923525,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
35,0.010243743307045949,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
35,0.01020401589320177,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
35,0.010227140805737932,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
35,0.010266275273106829,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
35,0.010239592681718947,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
40,0.010281834713541606,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
40,0.010283565273693122,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
40,0.010263375405258767,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
40,0.010249530924046638,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
40,0.010274335619551702,MLW_1_arabiensis_2015,MLW,1,arabiensis,2015
Loading