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decomverse / ACTIONet

ACTIONet single-cell analysis framework
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Error drawing with ACE2AnnData and plot.ACTIONet(ace) command #14

Open kazushin opened 3 years ago

kazushin commented 3 years ago

Hi,

I am trying to run the “Example Run” using ‘pbmc_10k_v3.h5’ based on your website’s tutorials. I have seen errors when I was drawing "plot.ACTIONet(ace, "celltypes", transparency.attr = ace$node_centrality)" and following "ACE2AnnData" to export the results.

Do you have any idea to solve the issues?

Am I something wrong or missing packages which need to be installed?

Thank you.

ace = import.ace.from.10X.h5('pbmc_10k_v3.h5', prefilter = T, min_cells_per_feat = 0.01, min_feats_per_cell = 1000) ace = normalize.ace(ace) ace = reduce.ace(ace)

Computing reduced ACTION kernel (sparse): Performing SVD on original matrix: IRLB_ (sparse) -- A: 12075 x 10744 Computing perturbed SVD ... done

ace = run.ACTIONet(ace) Running ACTION (14 threads): Iterating from k = 2 ... 40: 39/39 finished Joining trace of C & H matrices (depth = 40) ... done (819 archetypes) Pruning archetypes: Non-specific archetypes: 12 Unreliable archetypes: 72 Trivial archetypes: 73 Building adaptive network (14 threads): Parameters: density = 1.00, mutual_edges_only = TRUE Building index ... done Constructing k*-NN ... done Finalizing network ... done Computing layout (14 threads): Parameters: layout_epochs = 1000 Computing 2D layout ... done Computing 3D layout ... done Computing node colors ... done Unifying 667 archetypes (14 threads): Parameters: alpha = 0.99, sensitivity = 0.00 Running network diffusion 26 unified states (sensitivity = 0.70) Computing feature specificity ... done

data("curatedMarkers_human") markers = curatedMarkers_human$Blood$PBMC$Ding2019$marker.genes annot.out = annotate.cells.using.markers(ace, markers) ace$celltypes = annot.out$Labels plot.ACTIONet(ace, "celltypes", transparency.attr = ace$node_centrality)

Error in plot.ACTIONet(ace, "celltypes", transparency.attr = ace$node_centrality) : unused argument (transparency.attr = ace$node_centrality)

ACE2AnnData(ace, fname = "pbmc_10k_v3.h5ad")

Error in ACE2AnnData(ace, fname = "pbmc_10k_v3.h5ad") : unused argument (fname = "pbmc_10k_v3.h5ad")

plot.ACTIONet(ace) ACE2AnnData(ace, fname = "pbmc_10k_v3.h5ad")

Error in ACE2AnnData(ace, fname = "pbmc_10k_v3.h5ad") : unused argument (fname = "pbmc_10k_v3.h5ad")

sebastianpineda commented 3 years ago

Hi. It appears you're not using valid argument names. The R documentation (e.g. ?plot.ACTIONet) shows the appropriate argument names for passing transparency attributes, output file names, etc.

kazushin commented 3 years ago

Hi, the error comes up because of inappropriate argument names. I am going to try to put the appropriate argument names on it. Thank you very much for the comment. Let me try.