Giters

catavallejos / BASiCS

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data. This is an unstable experimental version. Please see http://bioconductor.org/packages/BASiCS/ for the official release version

Geek Repo:Geek Repo

Github PK Tool:Github PK Tool

Add horizontal reference lines to `BASiCS_DiagPlot` as default?

catavallejos opened this issue · comments

commented

Similar to what we did in the workflow:

diag_p1 <- BASiCS_DiagPlot(chain_sm, Measure = "geweke")
diag_p1 <- diag_p1 +
  geom_hline(yintercept = c(-3, 3), col = "firebrick", linetype = "dashed") +
  theme(legend.position = "none")
diag_p2 <- BASiCS_DiagPlot(chain_sm, Measure = "ess")
diag_p2 <- diag_p2 +
  geom_hline(yintercept = 100, col = "firebrick", linetype = "dashed") +
  theme(legend.position = "none")
diag_p1 + diag_p2 + plot_annotation(tag_levels = "A")
commented

Need to check the defaults, I know rhat of 1.05 is recommended for multi-chain rhat and we used abs(3) for geweke. I guess from this we used 100 for ESS