plot_genes2: Plot gene locations for genomic interval
In duytpm16/qtl2utils: Modification of QTL2 Plots

Description Description Usage Arguments Value Hidden graphics parameters

Modified version of qtl2's =plot_genes{plot_genes()} function to allow plotting of the haplotype's QTL peak (assuming the region is set around the peak) and to easily identify which gene the SNP with the highest LOD score overlap. See plot_snpasso2() description for more info.

Plot gene locations for a genomic interval, as rectangles with gene symbol (and arrow indicating strand/direction) below.

plot_genes2(genes,  scan1output , snpinfo, snp_lod, max_peak, haplo_peak_drop = NULL,
            minrow=4, padding=0.2,
            colors=c("black", "red3", "green4", "blue3", "darkorange2"),
            scale_pos=1, start_field="start", stop_field="stop",
            strand_field="strand", name_field="Name", ...)

`genes`	Data frame containing `start` and `stop` in Mbp, `strand` (as `"-"`, `"+"`, or `NA`), and `Name`.
`scan1output`	Output of `scan1()` using SNP probabilities derived by `genoprob_to_snpprob()`.
`snpinfo`	Data frame with SNP information with the following columns (the last three are generally derived from with `index_snps()`): `chr` - Character string or factor with chromosome `pos` - Position (in same units as in the `"map"` attribute in `genoprobs`. `sdp` - Strain distribution pattern: an integer, between 1 and 2^n - 2 where n is the number of strains, whose binary encoding indicates the founder genotypes `snp` - Character string with SNP identifier (if missing, the rownames are used). `index` - Indices that indicate equivalent groups of SNPs. `intervals` - Indexes that indicate which marker intervals the SNPs reside. `on_map` - Indicate whether SNP coincides with a marker in the `genoprobs`
`snp_lod`	Same as 'scan1output'.The scan1output may have been modified somewhere so this extra parameter was created to obtain the original SNP's LOD scores.
`max_peak`	Numeric value in Mbps of the location of the haplotype's QTL peak. This can be obtained from `max_scan1()` 'pos' column.
`haplo_peak_drop`	A vector of length two containing the range of Mbps that have LOD scores within the QTL peak drop. This vector should be the output from `lod_drop_rng()`.
`minrow`	Minimum number of rows of genes in the plot
`padding`	Proportion to pad with white space around the genes
`colors`	Vectors of colors, used sequentially and then re-used.
`scale_pos`	Factor by which to scale position (for example, to convert basepairs to Mbp)
`start_field`	Character string with name of column containing the genes' start positions.
`stop_field`	Character string with name of column containing the genes' stop positions.
`strand_field`	Character string with name of column containing the genes' strands.
`name_field`	Character string with name of column containing the genes' names.
`...`	Optional arguments passed to `graphics::plot()`.