track_plot | R Documentation |
Make gene track plot using Gviz
track_plot(
finemapstats,
region,
gene.annots,
bigSNP = NULL,
txdb = NULL,
counts = NULL,
peaks = NULL,
loops = NULL,
genome = "hg19",
filter_loop_genes = NULL,
filter_loop_snps = NULL,
filter_protein_coding_genes = TRUE,
color_piptrack_by = c("locus", "cs", "none"),
highlight_snps = NULL,
counts.ylim = c(0, 1),
counts.color,
peaks.color = "navy",
loops.color = "gray",
highlight.color = "pink",
genelabel.side = c("above", "below", "left", "right"),
track.sizes = NULL,
rotation.title = 0,
verbose = FALSE,
...
)
finemapstats |
A GRanges object of processed finemapping summary statistics |
region |
The genomic region to visualize in the format of "chr:start-end". |
gene.annots |
A GRanges object of gene annotations |
bigSNP |
A |
txdb |
A |
counts |
A list of counts data to display as quantitativ data tracks |
peaks |
A list of peaks to display as binary data tracks |
loops |
A list of chromatin loops, e.g. PC-HiC, ABC, etc. |
genome |
Genome assembly version (default: "hg19"). |
filter_loop_genes |
A vector of gene names. Only show loops connected to the genes. |
filter_loop_snps |
A vector of SNP IDs. Only show loops connected to the SNPs. |
filter_protein_coding_genes |
Logical. If TRUE, only shows protein coding gene. |
color_piptrack_by |
Color SNPs in the PIP track by
|
highlight_snps |
SNPs (rsIDs) to highlight. Or highlight top SNP ('topSNP'). |
counts.ylim |
ylim range (default: between 0 and 1) for the |
counts.color |
Colors for the |
peaks.color |
Colors for the |
highlight.color |
Colors for the highlighted SNPs |
genelabel.side |
Side to put gene labels, options are: 'above' (default), 'below', 'left', 'right'. |
track.sizes |
Sizes of the tracks |
rotation.title |
The rotation angle for the text in the track title |
verbose |
If TRUE, print detail messages for plotting |
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