Pca - cassav - with groups

using Jchemo, JchemoData
using JLD2, CairoMakie, GLMakie

Data importation

using JchemoData, JLD2, CairoMakie, GLMakie
path_jdat = dirname(dirname(pathof(JchemoData)))
db = joinpath(path_jdat, "data/cassav.jld2")
@load db dat
@names dat

(:X, :Y)

X = dat.X
@head X

... (280, 1050)

3×1050 DataFrame

950 columns omitted

Row	400	402	404	406	408	410	412	414	416	418	420	422	424	426	428	430	432	434	436	438	440	442	444	446	448	450	452	454	456	458	460	462	464	466	468	470	472	474	476	478	480	482	484	486	488	490	492	494	496	498	500	502	504	506	508	510	512	514	516	518	520	522	524	526	528	530	532	534	536	538	540	542	544	546	548	550	552	554	556	558	560	562	564	566	568	570	572	574	576	578	580	582	584	586	588	590	592	594	596	598	⋯
	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	Float64	⋯
1	0.399996	0.406522	0.413008	0.41958	0.426073	0.43219	0.438007	0.443949	0.44995	0.455081	0.45934	0.463535	0.467663	0.4711	0.473688	0.475809	0.477585	0.479175	0.480602	0.481708	0.482613	0.483457	0.484222	0.484873	0.485359	0.485729	0.486114	0.486469	0.486478	0.48599	0.485258	0.484175	0.482594	0.481078	0.48004	0.478911	0.477338	0.475769	0.474313	0.472419	0.470243	0.468227	0.465727	0.461779	0.456278	0.44993	0.442413	0.433093	0.422563	0.411268	0.399469	0.387154	0.374109	0.360391	0.346233	0.331832	0.317179	0.302623	0.288342	0.274052	0.260325	0.247976	0.236827	0.226326	0.216817	0.208673	0.201658	0.195395	0.189823	0.185099	0.181055	0.177544	0.174485	0.171748	0.169348	0.167329	0.165411	0.163188	0.161034	0.159611	0.158424	0.15692	0.155245	0.153579	0.151826	0.150128	0.148504	0.14687	0.145472	0.144396	0.143197	0.141824	0.140615	0.13959	0.138668	0.137875	0.137149	0.136432	0.135721	0.134834	⋯
2	0.460896	0.46706	0.475677	0.483438	0.490809	0.49877	0.506465	0.513268	0.519421	0.525145	0.530744	0.536144	0.540957	0.545328	0.549367	0.552727	0.555333	0.557708	0.560185	0.562357	0.563894	0.564909	0.565277	0.565188	0.565042	0.564877	0.564355	0.563649	0.563257	0.563012	0.562394	0.561379	0.560341	0.559398	0.558006	0.555778	0.553171	0.550812	0.548678	0.546616	0.544579	0.542149	0.538448	0.533893	0.529018	0.523422	0.516682	0.509148	0.501018	0.491444	0.480527	0.469045	0.456873	0.443933	0.430479	0.416739	0.402484	0.387522	0.372858	0.359546	0.347254	0.334975	0.322734	0.311426	0.301126	0.291658	0.282998	0.27483	0.266987	0.259567	0.25244	0.245352	0.238349	0.23153	0.224645	0.217789	0.211007	0.204099	0.197368	0.191349	0.185842	0.180374	0.17498	0.169971	0.165402	0.161085	0.156995	0.153294	0.150104	0.147443	0.145052	0.142827	0.140707	0.138663	0.136762	0.13506	0.133552	0.132191	0.130964	0.129819	⋯
3	0.464731	0.471416	0.47828	0.48733	0.497117	0.503004	0.505579	0.509316	0.514649	0.519317	0.523192	0.527309	0.531434	0.534748	0.537076	0.539033	0.540811	0.541883	0.542183	0.54232	0.542744	0.543293	0.543675	0.54372	0.543589	0.543868	0.544487	0.544648	0.544239	0.543642	0.542987	0.542122	0.541004	0.539853	0.538904	0.537862	0.536159	0.534021	0.532138	0.530054	0.527327	0.524462	0.521329	0.51703	0.511295	0.504519	0.496551	0.487221	0.476865	0.464969	0.451786	0.438225	0.424616	0.41058	0.395809	0.380595	0.365225	0.349705	0.334253	0.319378	0.305204	0.291255	0.277619	0.265214	0.25445	0.244907	0.236255	0.228498	0.221774	0.216081	0.210953	0.206254	0.202226	0.198769	0.195577	0.192592	0.189974	0.187627	0.185356	0.183314	0.181477	0.179274	0.176502	0.174001	0.172465	0.171099	0.169275	0.167275	0.165531	0.164022	0.162529	0.161149	0.160061	0.159114	0.157931	0.156577	0.155341	0.154278	0.153273	0.152306	⋯

Y = dat.Y
@head Y

... (280, 2)

3×2 DataFrame

Row	year	tbc
	Int64	Float64
1	2009	1.58068
2	2009	7.85516
3	2009	1.77595

year = Y.year
tab(year)

OrderedCollections.OrderedDict{Int64, Int64} with 5 entries:
  2009 => 42
  2010 => 47
  2011 => 40
  2012 => 71
  2013 => 80

Model fitting and scores T

model = pcasvd(nlv = 10)
fit!(model, X)  
fitm = model.fitm
@head T = fitm.T

3×10 Matrix{Float64}:
 -1.74085  -1.25003  -0.0913075  …  -0.0120857   0.0234582  -0.0483602
 -2.17482  -1.49341   0.591863      -0.0216646  -0.0135722  -0.0162003
 -1.58075  -1.37      0.35223       -0.0694361  -0.0282525  -0.0334348
... (280, 10)

2-D score spaces

CairoMakie.activate!()  
plotxy(T[:, 1], T[:, 2], year; zeros = true, xlabel = "PC1", ylabel = "PC2").f

lev = mlev(year)
nlev = length(lev)
color = cgrad(:Dark2_5, nlev; categorical = true, alpha = .7)
plotlv(T[:, 1:6], year; size = (750, 400), shape = (2, 3), color = color, zeros = true, 
    xlabel = "PC", ylabel = "PC").f

3-D score spaces

CairoMakie.activate!()  
#GLMakie.activate!()    # for interactive axe-rotation

i = 1
size = (600, 350)
plotxyz(T[:, i], T[:, i + 1], T[:, i + 2], year; size, color, markersize = 10, 
    xlabel = string("PC", i), ylabel = string("PC", i + 1), zlabel = string("PC", i + 2), 
    title = "Pca score space").f