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Results finalized and plots for publication in R

Analyses generated on Ilifu have now been finalized for publication. Plots for publication were generated in R based on these results
Added by Katie Lennard over 5 years ago

VF results used:
from Ilifu /cbio/users/katie/Nicol/Ps_aerug_srst2_MLST/VFDB_cov_80_diverge_10/srst2/Ps_VF_cov_80_ID_90_report_compiledResults.txt
AMR results used:
from Ilifu /cbio/users/katie/Nicol/Ps_aerug_srst2_MLST/AMR_cov_80_diverge_10/srst2/Ps_AMR_cov_80_ID_90_report_compiledResults.txt
MLST results used:
Manually curated MLST results as previously described
SNP-based phylogenetic tree used:
The 'core SNPs" phylogenetic tree generated in the Tychus alignment module was used to generate publication quality plots in R. This core SNPs tree was generated using kSNP3 and is built based on SNPs that are present in all isolates considered (from Ilifu /cbio/users/katie/Nicol/SNPsAndPhylogenies_Ps_ref_genome/Trees/tree.core.tre)

R plots (phylogenetic SNP tree with heatmap of VFs and AMRs) were generated using the R packages ggtree, ggimage, GeneMates (heatMapPAM() function) and multiple Fisher's exact tests and MTC was conducted with metagenomeSeq's fitPA() function

The attached plot was up to date on 3/9/19

heatMapPAM_VFs_rectangle_hclust_fisher_significant_plusAMR_PPT_v4.pdf (65.1 KB) heatMapPAM_VFs_rectangle_hclust_fisher_significant_plusAMR_PPT_v4.pdf Katie Lennard, 09/03/2019 01:49 PM

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