Error when running dynamics on dynast-preprocessed dataset

[Bastiaanspanjaard]

trafficstars

Hello,

Thanks for sharing your great work! I would love to use dynamo to analyze some of our data but I'm running into trouble.

I have ran dynast (dynast-release 1.0.1) to align and estimate labeling rates in single-cell metabolic labeling data. I can load this dataset into dynamo and preprocess it using

import dynamo as dyn
adata = dyn.read_h5ad('P1407_NM5_S10_estimate_adata.h5ad')
dyn.pp.recipe_monocle(adata)

The adata object has a lot of layers:

layers: 'X_l_TC', 'X_l_TC_est', 'X_n_TC', 'X_n_TC_est', 'ambiguous', 'labeled_TC', 'labeled_TC_est', 'sl_TC', 'sl_TC_est', 'sn_TC', 'sn_TC_est', 'spliced', 'total', 'ul_TC', 'ul_TC_est', 'un_TC', 'un_TC_est', 'unlabeled_TC', 'unlabeled_TC_est', 'unspliced', 'X_unspliced', 'X_spliced'

However, when I next run

dyn.tl.dynamics(adata, model='stochastic', cores=3, experiment_type = 'one-shot', 
                assumption_mRNA = 'ss', est_method = 'negbin')

(these are the parameters that made most sense for me - I have tried some other combinations but everything gave an error) I get the following error:

|-----> dynamics_del_2nd_moments_key is None. Using default value from DynamoAdataConfig: dynamics_del_2nd_moments_key=False
|-----------> removing existing M layers:[]...
|-----------> making adata smooth...
|-----> calculating first/second moments...
---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
Input In [6], in <cell line: 1>()
----> 1 dyn.tl.dynamics(adata, model='stochastic', cores=3, experiment_type = 'one-shot', 
      2                 assumption_mRNA = 'ss', est_method = 'negbin')

File ~/anaconda3/envs/dynamo/lib/python3.10/site-packages/dynamo/tools/dynamics.py:358, in dynamics(adata, filter_gene_mode, use_smoothed, assumption_mRNA, assumption_protein, model, est_method, NTR_vel, group, protein_names, concat_data, log_unnormalized, one_shot_method, fraction_for_deg, re_smooth, sanity_check, del_2nd_moments, cores, tkey, **est_kwargs)
    356         moments(adata, genes=valid_bools, group=group)
    357     else:
--> 358         moments(adata, genes=valid_bools, group=tkey)
    359 elif tkey is not None:
    360     main_warning(
    361         f"You used tkey {tkey} (or group {group}), but you have calculated local smoothing (1st moment) "
    362         f"for your data before. Please ensure you used the desired tkey or group when the smoothing was "
    363         f"performed. Try setting re_smooth = True if not sure."
    364     )

File ~/anaconda3/envs/dynamo/lib/python3.10/site-packages/dynamo/tools/moments.py:205, in moments(adata, X_data, genes, group, conn, use_gaussian_kernel, normalize, use_mnn, layers, n_pca_components, n_neighbors, copy)
    202 for layer2 in layers[i:]:
    203     layer_y = adata.layers[layer2].copy()
--> 205     layer_y_group = np.where([layer2 in x for x in [only_splicing, only_labeling, splicing_and_labeling]])[0][0]
    206     # don't calculate 2 moments among uu, ul, su, sl -
    207     # they should be time-dependent moments and
    208     # those calculations are model specific
    209     if (layer_x_group != layer_y_group) or layer_x_group == 2:

IndexError: index 0 is out of bounds for axis 0 with size 0

I would very much appreciate any help you can give here.

Thanks in advance, Bastiaan

[Xiaojieqiu]

thanks for using dynast and dynamo. Could you please just use the following layers:

adata_ntr.X = adata_ntr.layers['total']
adata_ntr.layers['new'] = adata_ntr.layers['labeled_TC'].copy()
adata_ntr.layers['total'] = adata_ntr.layers['labeled_TC'] + adata_ntr.layers['unlabeled_TC']
for layer in list(adata_ntr.layers.keys()):
    if layer not in ['new', 'total', 'spliced', 'unspliced']:
        del adata_ntr.layers[layer]
adata_ntr

Please also check out the dyn.tl.recipe_one_shot_data(adata)

[Bastiaanspanjaard]

Thanks, this got me a lot further!

I suppose that if I wanted to use dynast's estimation of the actual number of new transcripts (i.e. corrected for the labeling rate), I would have to use the layers 'labeled_TC_est' and 'unlabeled_TC_est', instead of 'unlabeled_TC' and 'unlabeled_TC', right?

[Xiaojieqiu]

that is right. Please also make sure you used the latest dynast to analyze the data

[github-actions[bot]]

This issue is stale because it has been open 90 days with no activity. Remove stale label or comment or this will be closed in 14 days

[Bastiaanspanjaard]

Comment to remove stale