HTTP Error Again

[Zhklu2003]

Hi Dr. Wang,

I was trying to download the dataset by

import cospar as cs adata_orig = cs.datasets.hematopoiesis()

But a HTTP error occurs since the url "https://kleintools.hms.harvard.edu/tools/downloads/cospar/LARRY_adata_preprocessed.h5ad" is now inaccessible,

And also there are some issues about gene_expression_dynamics function.

Could you check it? Thanks!

[ShouWenWang]

That is true. Please use the latest CoSpar in our github. This will work. git clone https://github.com/ShouWenWang-Lab/cospar python setup.py develop

-- Shou-Wen Wang, Ph.D. Principal Investigator School of Life Sciences | School of Science Westlake University Shilongshan ST #18, Xihu, Hangzhou, Zhejiang https://www.shouwenwang-lab.com/

From: Zhklu2003 @.> Date: Thursday, June 27, 2024 at 1:44 PM To: ShouWenWang-Lab/cospar @.> Cc: Subscribed @.***> Subject: [ShouWenWang-Lab/cospar] HTTP Error Again (Issue #11)

Hi Dr. Wang,

I was trying to download the dataset by

import cospar as cs adata_orig = cs.datasets.hematopoiesis()

But a HTTP error occurs since the url "https://kleintools.hms.harvard.edu/tools/downloads/cospar/LARRY_adata_preprocessed.h5ad" is now inaccessible,

And also there are some issues about gene_expression_dynamics function.

Could you check it? Thanks!

— Reply to this email directly, view it on GitHubhttps://github.com/ShouWenWang-Lab/cospar/issues/11, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABDCASX2NF7OJBVXLTDIXKDZJORDXAVCNFSM6AAAAABJ7F46V2VHI2DSMVQWIX3LMV43ASLTON2WKOZSGM3TOMJZG4ZDAMA. You are receiving this because you are subscribed to this thread.Message ID: @.***>

[Zhklu2003]

Thanks for help! Also, I have met a problem. When I run the code below

import cospar as cs adata_orig = cs.datasets.hematopoiesis_subsampled() adata = cs.tmap.infer_Tmap_from_multitime_clones( adata_orig, clonal_time_points=["2", "4"], later_time_point="6", smooth_array=[20, 15, 10, 5], sparsity_threshold=0.1, intraclone_threshold=0.2, max_iter_N=10, epsilon_converge=0.01, ) cs.tl.progenitor( adata, selected_fates=["Neutrophil","Monocyte"], source="transition_map", map_backward=True, bias_threshold_A=0.5, bias_threshold_B=0.5, sum_fate_prob_thresh=0.2, avoid_target_states=True, ) gene_name_list = ["Gata1", "Mpo", "Elane", "S100a8"] selected_fate = "Neutrophil" cs.pl.gene_expression_dynamics( adata, selected_fate, gene_name_list, traj_threshold=0.2, invert_PseudoTime=False, compute_new=True, gene_exp_percentile=99, n_neighbors=8, plot_raw_data=False, ) gene_name_list = ["Gata1", "Mpo", "Elane", "S100a8"] selected_fate = "Neutrophil" cs.pl.gene_expression_dynamics( adata, selected_fate, gene_name_list, traj_threshold=0.2, invert_PseudoTime=False, compute_new=True, gene_exp_percentile=99, n_neighbors=8, plot_raw_data=False, )

I will meet a type error TypeError: asarray() got an unexpected keyword argument 'copy'.

Could you give me some advice? Thanks.

[Zhklu2003]

And I am wondering if you have replication code online for this CoSpar paper? Some of figures and experiments cannot be found in https://cospar.readthedocs.io/.

Thanks!