Skip to content

6. Plotting

Jump to bottom
Sander W. van der Laan edited this page Aug 8, 2018 · 1 revision

Plotting prior to Meta-Analysis

Both the uncleaned and the cleaned reformatted GWAS data will be visualized: MetaGWASToolKit will generate various plots automagically:

  • Manhattan-plot
  • QQ-plot, regular with confidence interval
  • QQ-plot by coded allele frequency
  • QQ-plot by imputation quality
  • QQ-plot by variant type
  • a P-Z-plot showing the correlation between the observed p-values and the one calculated from 'beta' and the 'standard error'.
  • Histograms of the 'effect size', including lines at the ±4 standard deviation, and the 'imputation quality'.

Plotting after Meta-Analysis

After the meta-analysis is complete for each chunk, the data is checked, and if deemed okay, it will be concatenated into one file. After concatenation of the data, various plots of each model result for visual inspection (and publication) are made.

  • QQ-plots -- These are both regular including the total number and lambda, as well as stratified by coded allele frequency.
  • Manhattan-plots -- Good old Manhattan plots.
  • Effective Sample Size -- For the whole analysis the effective sample size will be calculated and plotted. Note: this script needs fixing. 🚧
  • SE-N-lambda -- Plotting the standard error accross cohorts as a function of sample size and inflation factor. Reference: Winkler T.W. et al.. Note: this script needs fixing. 🚧
  • LocusZoom plots -- After concatenation of the meta-analysis results, these will be clumped using the appropriate reference as downloaded (see above 'Installing the scripts locally'). Based on the particular clumping settings (indicated in metagwastoolkit.conf) regional association plots will be generated using an installment of LocusZoom v1.3. Note: this script needs fixing. 🚧
  • LocusTrack plots -- In addition to making LocusZoom plots (for which you will have to install LocusZoom) MetaGWASToolKit also generates files appropriate for LocusTrack plots; this online tool can plot many additional informative tracks underneath the regional association plot. Reference: Cuellar-Partida G. et al..
  • Genomic control -- Using the results from the fixed effects model, genomic control will be applied to the meta-analysis results. These lambda-corrected results will also be plotted (Manhattan, and [stratified] QQ-plots).

Note: The installation of LocusZoom v1.3 is required for this function to work.

The MIT License (MIT)

Copyright (c) 2015-2022 Sander W. van der Laan | s.w.vanderlaan [at] gmail [dot] com | swvanderlaan.github.io.

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Reference: http://opensource.org.

Clone this wiki locally