In the DIMA plot, there is an issue with highlighting and labeling genes that have differential expression. Genes with differential expressions are calculated using the DIMA calculation, and those genes are labeled with the i-modulon name. However, the scatterplot also uses the "line45_margin" feature, which colors all genes that has a greater log-fold change greater than a threshold. Thus, you sometimes get a situation where genes are colored but not labeled, which would be confusing for someone looking for which genes are highlighted. Removal of the "line45_margin" and replacement with defined groups in the call for the scatterplot function should fix the issue.
In the DIMA plot, there is an issue with highlighting and labeling genes that have differential expression. Genes with differential expressions are calculated using the DIMA calculation, and those genes are labeled with the i-modulon name. However, the scatterplot also uses the "line45_margin" feature, which colors all genes that has a greater log-fold change greater than a threshold. Thus, you sometimes get a situation where genes are colored but not labeled, which would be confusing for someone looking for which genes are highlighted. Removal of the "line45_margin" and replacement with defined groups in the call for the scatterplot function should fix the issue.