Arrow, directionality, line, smoothness

[wangjiawen2013]

Hi,
Could you explain the meaning of the arrow direction and the line ? Besides, some lines are smoothly, but some are very sharp, how do you draw the line ?

Are they (lines) similar to paga and monocle3 ? Lines overlap well with the main path of the graph, while sometimes the lines of VIA deviate from the centroid of the scatter points, is there a way to make it beautiful ?

[ShobiStassen]

For paga you have to compare with the viagraph For the draw-trajectory-gams the line that does not go through cells is because the 2D embedding does not capture all the information behind the higher dimensional gene space. monocle analysis is done on the 2D tsne/umap and not on the higher dimensional PCA/feature space. You can use the streamplots or plot_milestone_edgebundle functions to get trajectory projected more "directly" on the umap/tsne

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On Tue, 20 Dec 2022, 19:03 jiawen wang, ***@***.***> wrote: Hi, Could you explain the meaning of the arrow direction and the line ? Besides, some lines are smoothly, but some are very sharp, how do you draw the line ? Are they (lines) similar to paga and monocle3 ? Lines overlap well with the main path of the graph, while sometimes the lines of VIA deviate from the centroid of the scatter points, is there a way to make it beautiful ? [image: image] <https://user-images.githubusercontent.com/29703450/208640156-9d51c373-9e3f-417e-aee0-783ed4a4c6b8.png> — Reply to this email directly, view it on GitHub <#34>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AISI4SHVB5TTA5BIVNF6C4DWOF77ZANCNFSM6AAAAAATEJ5T3A> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[wangjiawen2013]

I cannot find the function plot_milestone_edgebundle, do you change it ? There is a similar one named plot_edge_bundle. But I haven't found any tutorial on plot_edge_bundle(). When I tried to used it with via.plot_edge_bundle(v0,text_labels=True), it displayed:
In [85]: via.plot_edge_bundle(v0,text_labels=True)

TypeError Traceback (most recent call last)
in
----> 1 via.plot_edge_bundle(v0,text_labels=True)

~/programs/miniconda3/envs/py37/lib/python3.7/site-packages/pyVIA/plotting_via.py in plot_edge_bundle(hammerbundle_dict, via_object, alpha_bundle_factor, linewidth_bundle, facecolor, cmap, extra_title_text, size_scatter, alpha_scatter, headwidth_bundle, headwidth_alpha, arrow_frequency, show_arrow, sc_labels_sequential, sc_labels_expression, initial_bandwidth, decay, n_milestones, scale_scatter_size_pop, show_milestones, sc_labels, text_labels)
735 milestone_numeric_values = df['sc_expression'].values # used to color edges
736 else:
--> 737 hammer_bundle = hammerbundle_dict['hammerbundle']
738 layout = hammerbundle_dict['milestone_embedding'][['x', 'y']].values
739 milestone_edges = hammerbundle_dict['edges']

TypeError: 'VIA' object is not subscriptable

[ShobiStassen]

Hi, Here is a sample usage in the rtd. You need to provide an embedding (ndarray) https://pyvia.readthedocs.io/en/latest/Hematopoiesis-scRNAseq.html

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On Tue, 20 Dec 2022, 20:27 jiawen wang, ***@***.***> wrote: I cannot find the function plot_milestone_edgebundle, do you change it ? There is a similar one named plot_edge_bundle. But I haven't found any tutorial on plot_edge_bundle(). When I tried to used it with via.plot_edge_bundle(v0,text_labels=True), it displayed: In [85]: via.plot_edge_bundle(v0,text_labels=True) TypeError Traceback (most recent call last) in ----> 1 via.plot_edge_bundle(v0,text_labels=True) ~/programs/miniconda3/envs/py37/lib/python3.7/site-packages/pyVIA/plotting_via.py in plot_edge_bundle(hammerbundle_dict, via_object, alpha_bundle_factor, linewidth_bundle, facecolor, cmap, extra_title_text, size_scatter, alpha_scatter, headwidth_bundle, headwidth_alpha, arrow_frequency, show_arrow, sc_labels_sequential, sc_labels_expression, initial_bandwidth, decay, n_milestones, scale_scatter_size_pop, show_milestones, sc_labels, text_labels) 735 milestone_numeric_values = df['sc_expression'].values # used to color edges 736 else: --> 737 hammer_bundle = hammerbundle_dict['hammerbundle'] 738 layout = hammerbundle_dict['milestone_embedding'][['x', 'y']].values 739 milestone_edges = hammerbundle_dict['edges'] TypeError: 'VIA' object is not subscriptable — Reply to this email directly, view it on GitHub <#34 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AISI4SAJ4YXXK7EWBIZIAMTWOGJ37ANCNFSM6AAAAAATEJ5T3A> . You are receiving this because you commented.Message ID: ***@***.***>

[ShobiStassen]

By the way, if you check out the tutorial on timeseries data in the RTD then you can see an example of how we modify the umap embedding to make it more consistent with the temporal chronology of the data :)

[wangjiawen2013]

Are the lines MCMC path ?

[ShobiStassen]

the lines in the plot_edge_bundle() are a fine-grained view of the intercellular connectivity highlighting all major pathways/connections. The weight of an edge means there are many cell-cell connections along this path. I will soon add in the functionality to highlight lineage probabilities from plot edge_bundle(). Currently you can color this graph by pseudotime, known temporal labels (for timeseries data) sc_labels_sequential (list, length nsamples), or gene expression sc_labels_expression (list length nsamples)