title: uwot is throwing an error running the Monocle3 R package's "find_gene_module()" function, likely as an issue with how my data is formatted
body: <p>I am trying to run the Monocle3 function find_gene_modules() on a cell_data_set (cds) but am getting a variety of errors in this. I have not had any other issues before this. I am working with an imported Seurat object. My first error came back stating that the number of rows were not the same between my cds and cds@preprocess_aux$gene_loadings values. I took a look and it seems my gene loadings were a list under cds@preprocess_aux@listData$gene_loadings. I then ran the following code to make a dataframe version of the gene loadings:</p>
  <pre><code>test &lt;- seurat@assays$RNA@counts@Dimnames[[1]]
  test &lt;- as.data.frame(test)
  cds@preprocess_aux$gene_loadings &lt;- test
  rownames(cds@preprocess_aux$gene_loadings) &lt;- cds@preprocess_aux$gene_loadings[,1]
  </code></pre>
  <p>Which created a cds@preprocess_aux$gene_loadings dataframe with the same number of rows and row names as my cds. This resolved my original error but now led to a new error being thrown from uwot as:</p>
  <pre><code>15:34:02 UMAP embedding parameters a = 1.577 b = 0.8951
  Error in uwot(X = X, n_neighbors = n_neighbors, n_components = n_components,  : 
    No numeric columns found
  </code></pre>
  <p>Running traceback() produces the following information.</p>
  <pre><code>&gt; traceback()
  4: stop(&quot;No numeric columns found&quot;)
  3: uwot(X = X, n_neighbors = n_neighbors, n_components = n_components, 
         metric = metric, n_epochs = n_epochs, alpha = learning_rate, 
         scale = scale, init = init, init_sdev = init_sdev, spread = spread, 
         min_dist = min_dist, set_op_mix_ratio = set_op_mix_ratio, 
         local_connectivity = local_connectivity, bandwidth = bandwidth, 
         gamma = repulsion_strength, negative_sample_rate = negative_sample_rate, 
         a = a, b = b, nn_method = nn_method, n_trees = n_trees, search_k = search_k, 
         method = &quot;umap&quot;, approx_pow = approx_pow, n_threads = n_threads, 
         n_sgd_threads = n_sgd_threads, grain_size = grain_size, y = y, 
         target_n_neighbors = target_n_neighbors, target_weight = target_weight, 
         target_metric = target_metric, pca = pca, pca_center = pca_center, 
         pca_method = pca_method, pcg_rand = pcg_rand, fast_sgd = fast_sgd, 
         ret_model = ret_model || &quot;model&quot; %in% ret_extra, ret_nn = ret_nn || 
             &quot;nn&quot; %in% ret_extra, ret_fgraph = &quot;fgraph&quot; %in% ret_extra, 
         batch = batch, opt_args = opt_args, epoch_callback = epoch_callback, 
         tmpdir = tempdir(), verbose = verbose)
  2: uwot::umap(as.matrix(preprocess_mat), n_components = max_components, 
         metric = umap.metric, min_dist = umap.min_dist, n_neighbors = umap.n_neighbors, 
         fast_sgd = umap.fast_sgd, n_threads = cores, verbose = verbose, 
         nn_method = umap.nn_method, ...)
  1: find_gene_modules(cds[pr_deg_ids, ], reduction_method = &quot;UMAP&quot;, 
         max_components = 2, umap.metric = &quot;cosine&quot;, umap.min_dist = 0.1, 
         umap.n_neighbors = 15L, umap.fast_sgd = FALSE, umap.nn_method = &quot;annoy&quot;, 
         k = 20, leiden_iter = 1, partition_qval = 0.05, weight = FALSE, 
         resolution = 0.001, random_seed = 0L, cores = 1, verbose = T)
  </code></pre>
  <p>I really have no idea what I am doing wrong or how to proceed from here. Does anyone with experience with uwot know where my error is coming from? Really appreciate the help!</p>