How to generate genotype data for gheatmap function in ggtree package
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2.5 years ago
shadowstep • 0

I followed the nCov course in biostar handbook, I did the following in command line using the nCov genomes from NCBI database:

nCov=NC_045512.fa

minimap2 -a $nCov nCov-genomes.fa | samtools sort > nCov-align.bam

# Index the alignments
samtools index nCov-align.bam

# Compute the genotypes from the alignment file with pileup.
bcftools mpileup -B -Ovu -f $nCov nCov-align.bam > nCov-genotypes.vcf

cat nCov-variants.vcf | bcftools query -f '%CHROM %POS %REF %ALT\n' > nCov-variants.txt

The results showed that there are variants at five positions

NC_045512 8782 C T
NC_045512 17747 C T
NC_045512 17858 A G
NC_045512 18060 C T
NC_045512 28144 T C

I also built and plotted a phylo tree for all these genomes using ggtree. Now If I want to use gheatmap() function to show the variants at each position and map it to the phylotree, how can I generate a genotype matrix that meets the requirement of gheatmap()?

I want to make a plot like this:

enter image description here

This function requires a genotype matrix like this:

PB2 PB1 PA  HA  NP  NA  M   NS
A/Swine/Binh_Duong/03_10/2010   trig    trig    trig    HuH3N2  trig    HuH3N2  trig    trig
A/Swine/Binh_Duong/03_08/2010   trig    trig    trig    HuH3N2  trig    HuH3N2  trig    trig
A/Swine/HK/2857/2011    pdm pdm pdm HuH3N2  trig    HuH3N2  pdm pdm
A/Swine/HK/1071/2012    pdm pdm pdm HuH3N2  trig    HuH3N2  pdm pdm
A/Swine/HK/2454/2012    pdm pdm pdm HuH3N2  trig    HuH3N2  pdm pdm
A/Swine/GX_NS2783/2010  pdm pdm pdm HuH3N2  pdm HuH3N2  pdm pdm
A/Swine/HK_NS2733/2012  pdm pdm pdm HuH3N2  pdm HuH3N2  pdm pdm
A/Swine/HK_NS2439/2011  pdm pdm pdm HuH3N2  pdm HuH3N2  pdm pdm
A/Swine/HK/2503/2011    pdm pdm pdm HuH3N2  pdm HuH3N2  pdm pdm
A/Swine/GX/2803/2011    pdm trig    pdm HuH3N2  pdm HuH3N2  pdm pdm
A/Swine/GX_NS3108/2011  pdm trig    pdm HuH3N2  pdm HuH3N2  pdm pdm
A/Swine/GX_NS3106/2011  pdm trig    pdm HuH3N2  pdm HuH3N2  pdm pdm
ggtree genome SNP alignment R • 960 views
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