Generalized Procrustes analysis

import numpy as np
import pandas as pd

import matplotlib.pyplot as plt
import seaborn as sns

from sklearn.decomposition import PCA

from ktch.datasets import load_landmark_mosquito_wings
from ktch.landmark import GeneralizedProcrustesAnalysis

Load mosquito wing landmark dataset

from Rohlf and Slice 1990 Syst. Zool.

data_landmark_mosquito_wings = load_landmark_mosquito_wings(as_frame=True)
data_landmark_mosquito_wings.coords

		x	y
specimen_id	coord_id
1	0	-0.4933	0.0130
	1	-0.0777	0.0832
	2	0.2231	0.0861
	3	0.2641	0.0462
	4	0.2645	0.0261
...	...	...	...
127	13	-0.2028	0.0371
	14	0.0490	0.0347
	15	-0.0422	0.0204
	16	0.1004	-0.0180
	17	-0.1473	-0.0057

2286 rows × 2 columns

fig, ax = plt.subplots()
sns.scatterplot(
    data = data_landmark_mosquito_wings.coords,
    x="x",y="y", 
    hue="specimen_id", style="coord_id",ax=ax
    )
ax.set_aspect('equal')
ax.legend(loc="upper left", bbox_to_anchor=(1, 1))

<matplotlib.legend.Legend at 0x7f6b1aaaead0>

For applying generalized Procrustes analysis (GPA), we convert the configuration data into DataFrame of shape n_specimens x (n_landmarks*n_dim).

df_coords = data_landmark_mosquito_wings.coords.unstack().swaplevel(1, 0, axis=1).sort_index(axis=1)
df_coords.columns = [dim +"_"+ str(landmark_idx) for landmark_idx,dim in df_coords.columns]
df_coords

	x_0	y_0	x_1	y_1	x_2	y_2	x_3	y_3	x_4	y_4	...	x_13	y_13	x_14	y_14	x_15	y_15	x_16	y_16	x_17	y_17
specimen_id
1	-0.4933	0.0130	-0.0777	0.0832	0.2231	0.0861	0.2641	0.0462	0.2645	0.0261	...	-0.1768	0.0341	0.0715	0.0509	-0.0540	0.0238	0.0575	-0.0059	-0.1401	-0.0240
2	-0.4814	0.0135	-0.0058	0.0780	0.2345	0.0644	0.2460	0.0467	0.2487	0.0281	...	-0.1808	0.0229	0.0484	0.0405	-0.0519	0.0164	0.0623	-0.0047	-0.1444	-0.0286
3	-0.4622	0.0159	0.0089	0.0689	0.2404	0.0545	0.2501	0.0424	0.2600	0.0230	...	-0.1724	0.0182	0.0577	0.0344	-0.0468	0.0115	0.0766	-0.0079	-0.1602	-0.0162
4	-0.4534	-0.0028	-0.0318	0.0738	0.2423	0.0808	0.2627	0.0559	0.2654	0.0322	...	-0.1536	0.0150	0.0617	0.0436	-0.0549	0.0217	0.0705	-0.0031	-0.1507	-0.0273
5	-0.4926	-0.0212	-0.0260	0.0708	0.2347	0.0679	0.2398	0.0584	0.2415	0.0355	...	-0.1374	0.0154	0.0762	0.0457	-0.0313	0.0170	0.0880	0.0037	-0.1318	-0.0278
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
123	-0.4703	-0.0009	0.0011	0.0805	0.2146	0.0747	0.2348	0.0585	0.2453	0.0350	...	-0.1624	0.0193	0.0557	0.0467	-0.0272	0.0190	0.0718	-0.0052	-0.1583	-0.0251
124	-0.4725	0.0441	0.0318	0.0808	0.2382	0.0419	0.2504	0.0237	0.2492	0.0019	...	-0.1724	0.0390	0.0667	0.0418	-0.0108	0.0205	0.0548	-0.0049	-0.1546	-0.0115
125	-0.4697	0.0196	0.0007	0.0850	0.2228	0.0760	0.2485	0.0540	0.2548	0.0319	...	-0.1816	0.0213	0.0376	0.0408	-0.0073	0.0137	0.0592	-0.0103	-0.1531	-0.0300
126	-0.4620	0.0204	0.0082	0.0893	0.2061	0.0797	0.2374	0.0529	0.2457	0.0306	...	-0.1876	0.0241	0.0279	0.0403	-0.0425	0.0145	0.0729	-0.0123	-0.1460	-0.0269
127	-0.4570	0.0468	-0.0090	0.0753	0.2381	0.0463	0.2556	0.0275	0.2614	0.0064	...	-0.2028	0.0371	0.0490	0.0347	-0.0422	0.0204	0.1004	-0.0180	-0.1473	-0.0057

127 rows × 36 columns

GPA

gpa = GeneralizedProcrustesAnalysis().set_output(transform="pandas")

df_shapes = gpa.fit_transform(df_coords)
df_shapes

	x_0	y_0	x_1	y_1	x_2	y_2	x_3	y_3	x_4	y_4	...	x_13	y_13	x_14	y_14	x_15	y_15	x_16	y_16	x_17	y_17
specimen_id
1	-0.488913	0.021159	-0.075651	0.083813	0.222655	0.081657	0.262641	0.041408	0.262701	0.021471	...	-0.174735	0.036786	0.071747	0.049290	-0.053145	0.024519	0.056916	-0.006796	-0.139317	-0.021437
2	-0.479850	0.030667	-0.002995	0.078029	0.236289	0.055873	0.247131	0.037801	0.249161	0.019145	...	-0.179578	0.029304	0.049746	0.038675	-0.051194	0.018213	0.062000	-0.006922	-0.145098	-0.023383
3	-0.461238	0.021194	0.009668	0.068674	0.240606	0.051631	0.250150	0.039440	0.259809	0.019959	...	-0.171907	0.020150	0.057987	0.033671	-0.046599	0.012014	0.076367	-0.008775	-0.160124	-0.014332
4	-0.451582	0.021733	-0.027671	0.075199	0.245617	0.067345	0.264582	0.041450	0.265988	0.017707	...	-0.152122	0.023242	0.063790	0.040074	-0.053488	0.024575	0.070026	-0.006899	-0.151522	-0.019031
5	-0.491092	0.019428	-0.020015	0.072475	0.238724	0.048169	0.243009	0.038313	0.242816	0.015425	...	-0.135231	0.026596	0.079447	0.039142	-0.029701	0.019466	0.087717	-0.003550	-0.133219	-0.016779
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
123	-0.468839	0.028646	0.006143	0.080164	0.218584	0.060969	0.237700	0.043553	0.246690	0.019470	...	-0.160671	0.029436	0.058442	0.043044	-0.025929	0.020642	0.071228	-0.009699	-0.159374	-0.015077
124	-0.473804	0.016670	0.027045	0.082425	0.235150	0.055559	0.248370	0.038112	0.248433	0.016301	...	-0.174200	0.028931	0.064108	0.045546	-0.011957	0.019822	0.054939	-0.001719	-0.153528	-0.020407
125	-0.468449	0.032047	0.002958	0.084844	0.224473	0.069955	0.249549	0.047306	0.255251	0.025073	...	-0.180752	0.026088	0.038626	0.039732	-0.006925	0.013867	0.058834	-0.011863	-0.153659	-0.025890
126	-0.459471	0.036434	0.011277	0.088662	0.208061	0.072197	0.238303	0.044411	0.245792	0.021909	...	-0.186025	0.030549	0.029190	0.039168	-0.041832	0.015925	0.072178	-0.014794	-0.146368	-0.021701
127	-0.457745	0.025260	-0.012492	0.074647	0.235186	0.057309	0.253511	0.039387	0.260281	0.018625	...	-0.203892	0.027493	0.047226	0.036891	-0.043017	0.018365	0.100931	-0.013236	-0.146563	-0.012573

127 rows × 36 columns

We create a DataFrame, called df_shapes_vis, of shape (n_specimens*n_landmarks) x n_dim to visualize the aligned shapes.

df_shapes_vis = df_shapes.copy()
df_shapes_vis.columns = pd.MultiIndex.from_tuples([[int(landmark_idx), dim] for dim, landmark_idx in [idx.split("_") for idx in df_shapes_vis.columns]], names=["coord_id","dim"])
df_shapes_vis.sort_index(axis=1, inplace=True)
df_shapes_vis = df_shapes_vis.swaplevel(0,1,axis=1).stack(level=1)
df_shapes_vis

/tmp/ipykernel_1935/3231015902.py:4: FutureWarning: The previous implementation of stack is deprecated and will be removed in a future version of pandas. See the What's New notes for pandas 2.1.0 for details. Specify future_stack=True to adopt the new implementation and silence this warning.
  df_shapes_vis = df_shapes_vis.swaplevel(0,1,axis=1).stack(level=1)

	dim	x	y
specimen_id	coord_id
1	0	-0.488913	0.021159
	1	-0.075651	0.083813
	2	0.222655	0.081657
	3	0.262641	0.041408
	4	0.262701	0.021471
...	...	...	...
127	13	-0.203892	0.027493
	14	0.047226	0.036891
	15	-0.043017	0.018365
	16	0.100931	-0.013236
	17	-0.146563	-0.012573

2286 rows × 2 columns

fig, ax = plt.subplots()
sns.scatterplot(
    data = df_shapes_vis,
    x="x",y="y", 
    hue="specimen_id", style="coord_id",ax=ax
    )
ax.set_aspect('equal')
ax.legend(loc="upper left", bbox_to_anchor=(1, 1))

<matplotlib.legend.Legend at 0x7f6b6cd54dd0>

PCA

pca = PCA(n_components=10).set_output(transform="pandas")
df_pca = pca.fit_transform(df_shapes)

df_pca = df_pca.join(data_landmark_mosquito_wings.meta)
df_pca

	pca0	pca1	pca2	pca3	pca4	pca5	pca6	pca7	pca8	pca9	genus
specimen_id
1	-0.003856	0.093210	-0.029908	-0.049589	0.007598	0.042657	-0.005370	0.010359	-0.011595	0.034991	AN
2	-0.029857	0.023434	-0.006114	0.017268	0.014229	0.014271	0.013344	0.021849	-0.011211	0.005069	AN
3	-0.012572	0.019728	0.034610	0.025665	0.005116	-0.017905	0.008511	-0.004312	0.001597	0.009884	AN
4	-0.001652	0.049890	0.034137	0.001013	-0.019706	-0.010102	-0.001692	-0.010425	0.021595	-0.006472	AN
5	0.026869	0.032989	-0.010228	0.051852	-0.016741	0.023749	0.015917	-0.000273	-0.013100	0.012755	AN
...	...	...	...	...	...	...	...	...	...	...	...
123	-0.007864	0.009853	0.006369	0.026082	0.025424	0.013786	-0.009967	-0.018669	0.000513	-0.005515	CX
124	-0.005360	-0.014451	0.014347	0.013199	-0.000102	0.001379	-0.002919	-0.009755	-0.020409	-0.017790	CX
125	-0.030056	-0.000885	-0.013455	-0.000542	0.008940	0.008503	-0.021390	-0.014563	-0.003408	-0.010083	CX
126	-0.048757	0.000199	-0.024147	0.029841	0.040190	0.013335	0.000598	0.016086	0.018985	0.004560	DE
127	-0.017155	0.030018	0.001935	0.014438	0.014540	-0.035565	-0.011888	0.017324	-0.009739	0.012342	DE

127 rows × 11 columns

fig, ax = plt.subplots()
sns.scatterplot(
    data=df_pca, x="pca0", y = "pca1", 
    hue="genus",palette="Paired",
    ax=ax
    )
ax.legend(loc="upper left", bbox_to_anchor=(1, 1))

<matplotlib.legend.Legend at 0x7f6b2da15750>