brgew

Results 28 comments of brgew

interpretation of trajectory and batch effect

Is this resolved?

What does the grey color mean in the picture plotted by plot_cells based on one selected gene?

Hi, The legend on the right side of the plot shows that cells with zero expression (or less than zero) are colored gray so the gray cells have no expression....

Question : plot_genes_in_pseudotime / Module

Hi, I believe that you can subset the `cds` by the genes in your gene module and pass that subset to `plot_genes_pseudotime()`. Does this answer your question?

Error in cluster_cells function

Hi, Could you try reinstalling leidenbase and Monocle3 in R running in a terminal, and then try the cluster_cells again, again running R in a terminal. Perhaps, there is an...

error in cluster_cells: Error in graph.adjacency.dense(adjmatrix, mode = mode, weighted = weighted

Hi, There is a new Monocle3 version, 1.3.6, that should fix this problem when using recent igraph package versions.

object 'Dim_validate' not found

Hi, I am unable to reproduce this error without an example data set. Can you make a small example cds that reproduces the error and send it to me? I...

Problem with conda package build

Hi, I don't know how I can help with this problem.

Problem with conda package build

Hi, Is this issue resolved? Thank you, Brent

`fit_models` and `model_formula_str`

Hi, Do you need to use a formula that causes Monocle3 to fail? If you are curious, you can examine the code for `fit_models()` in the file monocle3/R/expr_models.R. Best Wishes,...

Different results when using violin plots and dot plots

Hi, Thank you for the feedback. This is interesting to me. I found that `plot_genes_violin()` uses ggplot2 to make the violin plots and when the data are log-transformed ggplot2 drops...