Dr. Tong Zhou

Same error while resampled sequence without gap

The default color set has 40 colors, please use the biggest color set by adding the parameter: color="wesanderson"

Please show me the full code pipeline and example data files. The Phylum_color object looks like a custom defined in the above code lines.

Dear wanxn518, Thank you for using itol.toolkit. Based on the commands, I suspect the issue may be due to the column for setting color being larger than 75. If possible,...

Hi Thanks for using itol.toolkit. The method mentioned in the [paper](https://www.sciencedirect.com/science/article/abs/pii/S0269749122014579) is choosing the most abundant OTU/ASV in the bin to build a tree. Best, Tong

I reviewed the code in the zip file provided. It only demonstrates template generation for tree coloring, but does not include implementation of the tree collapse method. You can refer...

I guess the meta_df object is a data.frame, if use data.table::fread will solve this problem. The tibble is a better format than data.frame in this case because they don't have...

Hi XiaoNan, Regarding your question, there is an example that demonstrates how to rename internal node labels: Lines 1773-1807 in the GitHub repository at https://github.com/TongZhou2017/itol.toolkit/blob/d2eac45180be6336b5acb949e21e4ba0738eb4a8/R/user.R#L1773. In phylogenetic tree files, internal...

I see, for the tree in dataset1, you can use the L1773 function which automatically adds internal node labels when clustering by group model. This is an important point -...

Could you share an example file of DATASET_HEATMAP without data part？