R: Plotting MSMC PSMC results using ggplot2 - Biostar: S I have finished my coalescent simulation analysis for all my populations, and now want to plot the results using ggplot, but I don't know how to parameterise it so that it matches the expectations for such a plot type
Ploting the PSMC results using R Data pre-processing steps for PSMC; Alright, Let’s run the actual things - PSMC; Ploting the PSMC results using R
Applying PSMC to simulated data - willyrv. github. io Once the psmc analysis is finished, you can plot the results 4-) Run: plot_results py And you will finally get a figure with the inferred demographic history (dashed blue line) and the real history (continuous black line) corresponding to the ms command
A practical introduction to sequentially Markovian coalescent methods . . . Looking backwards in time, the plots become identical from about 100–120 thousand years ago, indicating a shared population history The dotted line shows a PSMC plot from a hybrid genome constructed from the X chromosomes of the Yoruba and Chinese genomes, scaled by 0 75
DDLS Population genomics in practice - PSMC Just run plot_results py at the directory with the script and the psmc file This script was written to output a PDF file with the real population history (one of the benefits of using simulations) and the PSMC estimate
GitHub - lh3 psmc: Implementation of the Pairwise Sequentially . . . You may run `psmc2history pl' combined with `history2ms pl' to generate the ms command line that simulates the history inferred by PSMC, or visualize the result with `psmc_plot pl' To perform bootstrapping, one has to run splitfa first to split long chromosome sequences to shorter segments