Skip to content

GitLab

  • Menu
Projects Groups Snippets
    • Loading...
  • Help
    • Help
    • Support
    • Community forum
    • Submit feedback
    • Contribute to GitLab
  • Sign in
  • N ngs_tools
  • Project information
    • Project information
    • Activity
    • Labels
    • Members
  • Repository
    • Repository
    • Files
    • Commits
    • Branches
    • Tags
    • Contributors
    • Graph
    • Compare
  • Issues 15
    • Issues 15
    • List
    • Boards
    • Service Desk
    • Milestones
  • Deployments
    • Deployments
    • Releases
  • Monitor
    • Monitor
    • Incidents
  • Analytics
    • Analytics
    • Repository
    • Value stream
  • Activity
  • Graph
  • Create a new issue
  • Commits
  • Issue Boards
Collapse sidebar
  • bioinfo
  • ngs_tools
  • Issues
  • #85

Closed
Open
Created Mar 13, 2020 by domingue@domingueMaintainer

Hardcoded pvalue in plot

In the MA plot section "MA and Volcano plots" the description reads:

Each gene is represented with a dot. Genes with an adjusted p value below a certain threshold are shown in cyan (True)

However the code for adding color is using pvalue instead of padj and uses a harcoded value of 0.05:

https://git.mpi-cbg.de/bioinfo/ngs_tools/blob/master/dge_workflow/featcounts_deseq_mf.R#L576

deResults %>% ggplot(aes(0.5 * log2(mean_norm_count_1 * mean_norm_count_2), log2(mean_norm_count_2 / mean_norm_count_1), color = pvalue < 0.05)) +
    geom_point(alpha = 0.1) +
    geom_hline(yintercept = 0, color = "red") +
    facet_grid(condition_1 ~ condition_2)

pvalue_maplot

Expected behaviour Genes coloured by is_hit which reflects the cut-off used in arguments (qcutoff or pcutoff).

Assignee
Assign to
Time tracking