Homology: Constella

Group pseudo-landmarks into homology groupings

plantcv.homology.constella(cur_plms, pc_starscape, group_iter, outfile_prefix)

returns dataframe of grouped pseudo-landmarks and a group ID counter

  • Parameters:
    • cur_plms - A pandas array of plm multivariate space representing capturing two adjacent frames in a time series or otherwise analogous dataset in order to enable homology assignments
    • pc_starscape - PCA results from starscape
    • group_iter - Group ID counter
    • outfile_prefix - User defined file path and prefix name for output graphics
  • Context:
    • Used to group pseudo-landmarks into homology groupings
  • Example use:

from plantcv import plantcv as pcv

# Set global debug behavior to None (default), "print" (to file), 
# or "plot" (Jupyter Notebooks or X11)

pcv.params.debug = "print"

cur_plms, group_iter = pcv.homology.constella(cur_plms=cur_plms, pc_starscape=starscape_df, 
                                              group_iter=group_iter, outfile_prefix="./B100_d10_d11")

cur_plms

#       group   plmname             filename        plm_x   plm_y   SS_x    SS_y    TS_x    TS_y    CC_ratio    bot_left_dist   bot_right_dist  top_left_dist   top_right_dist  centroid_dist   orientation centroid_orientation
# 0     8       B100_rep1_d10_plm1  B100_rep1_d10   901     1151    892     1173    885     1167    255.000000  521.647390      404.545424      331.185748      35.000000       284.613773      -146.659293 155.506063
# 1     7       B100_rep1_d10_plm2  B100_rep1_d10   787     1425    789     1401    773     1405    6.219512    252.103153      187.416648      371.295031      330.800544      15.524175       -15.255119  14.931417
# 2     6       B100_rep1_d10_plm3  B100_rep1_d10   571     1344    594     1338    595     1342    255.000000  211.000000      409.538765      221.000000      414.779459      222.036033      99.659893   -72.707551
# 3     2       B100_rep1_d10_plm4  B100_rep1_d10   793     1523    796     1511    783     1519    18.888889   224.294449      132.909744      457.475682      420.286807      113.441615      -23.629378  5.057249
# 4     3       B100_rep1_d10_plm5  B100_rep1_d10   712     1511    736     1508    736     1512    255.000000  147.705789      214.560015      412.825629      441.184769      123.458495      92.385944   -144.893921
# 5     1       B100_rep1_d10_plm6  B100_rep1_d10   803     1555    795     1533    807     1532    255.000000  232.000000      119.000000      490.354973      448.090393      146.372812      -5.079608   7.853313
# 6     5       B100_rep1_d10_plm7  B100_rep1_d10   922     1415    898     1420    898     1416    255.000000  377.890196      140.000000      456.579675      292.000000      139.089899      -97.125016  87.939889
# 7     4       B100_rep1_d10_plm8  B100_rep1_d10   803     1478    816     1459    801     1454    12.207447   244.444268      141.739197      424.086076      374.414209      70.880181       165.650668  16.389540
# 8     8       B100_rep1_d11_plm1  B100_rep1_d11   912     1123    904     1146    895     1139    255.000000  550.368059      432.115725      341.000000      10.000000       314.658545      -147.339087 155.797162
# 9     9       B100_rep1_d11_plm2  B100_rep1_d11   786     1370    794     1347    784     1346    0.000000    283.637092      229.610540      327.466029      281.966310      40.112342       172.724995  175.710847
# 10    10      B100_rep1_d11_plm3  B100_rep1_d11   752     1236    761     1258    754     1260    255.000000  366.772409      361.470607      213.377600      204.129861      176.739922      13.448615   -10.101876
# 11    7       B100_rep1_d11_plm4  B100_rep1_d11   783     1427    781     1403    770     1406    32.692308   247.644907      188.957667      370.621100      334.270848      17.000000       -18.434949  0.000000
# 12    6       B100_rep1_d11_plm5  B100_rep1_d11   576     1353    598     1342    599     1347    255.000000  202.061872      400.649473      230.054341      415.470817      214.704448      110.695451  -74.604451
# 13    2       B100_rep1_d11_plm6  B100_rep1_d11   790     1525    791     1509    780     1517    23.448276   221.045244      135.366170      457.782700      423.117005      115.212847      -20.556045  3.483271
# 14    3       B100_rep1_d11_plm7  B100_rep1_d11   706     1510    729     1505    730     1509    255.000000  142.302495      220.637712      409.870711      443.198601      126.210142      97.275005   -142.403729
# 15    1       B100_rep1_d11_plm8  B100_rep1_d11   802     1553    791     1532    801     1530    255.000000  231.008658      120.016666      488.119862      446.430286      144.256716      -15.255119  7.568397
# 16    5       B100_rep1_d11_plm9  B100_rep1_d11   914     1417    891     1423    890     1417    255.000000  369.720164      138.231690      451.757678      294.108823      131.186890      -97.275005  86.941302
# 17    4       B100_rep1_d11_plm10 B100_rep1_d11   798     1475    809     1464    795     1458    0.000000    240.684441      147.566934      418.847228      373.202358      66.708320       164.054604  12.994617

Dendrogram

Screenshot

Source Code: Here