plot_facets | R Documentation |
Generate the following plots:
Log-ratio: Copy-number segmentation based on tumor-normal read coverage comparison.
Allelic imbalance: Allelic imbalance based on somatic changes in zygosity of heterozygous SNPs in the normal.
Integer copy number: Inference of the major and minor copy-number states based on the tumor-normal log ratio and allelic content.
Cellular fraction: Estimate of fraction of cells in sample harboring each segment.
cnlr_plot(facets_data, colors = c("#0080FF", "#4CC4FF"), plotX = FALSE, genome = c("hg19", "hg18", "hg38"), highlight_gene = NULL, adjust_diplogr = TRUE, subset_snps = NULL, return_object = FALSE) valor_plot(facets_data, colors = c("#0080FF", "#4CC4FF"), plotX = FALSE, genome = c("hg19", "hg18", "hg38"), highlight_gene = NULL, subset_snps = NULL, return_object = FALSE) cf_plot(facets_data, method = c("em", "cncf"), plotX = FALSE, genome = c("hg19", "hg18", "hg38"), return_object = FALSE) icn_plot(facets_data, method = c("em", "cncf"), plotX = FALSE, genome = c("hg19", "hg18", "hg38"), highlight_gene = NULL, return_object = FALSE) closeup_plot(facets_data, highlight_gene = NULL, plot_chroms = NULL, method = c("em", "cncf"), genome = c("hg19", "hg18", "hg38"), return_object = FALSE)
facets_data |
Output object from |
colors |
Vector of two colors for alternating chromosomes. |
plotX |
If |
genome |
Genome build. |
highlight_gene |
Highlight gene(s), provide gene symbol or mapped positions (internally). |
adjust_diplogr |
Normalize by sample dipLogR. |
subset_snps |
Subset the SNP profile to reduce weight of plotting, supply a factor by which to reduce or |
return_object |
If |
method |
When available, choose between plotting solution from |
plot_chroms |
Chromosomes to plot when using |
ggplot2
objects, see input parameter return_object
.
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