Visualization of Tm values
# Generate sample data with 150 sequences
set.seed(123)
# Generate 100 sequences for chr1
chr1_starts <- sort(sample(1:249250621, 100)) # chr1 length in hg19
chr1_lengths <- sample(50:200, 100, replace=TRUE)
chr1_ends <- chr1_starts + chr1_lengths
chr1_tms <- runif(100, min=60, max=80)
# Generate 50 sequences for chr2
chr2_starts <- sort(sample(1:243199373, 50)) # chr2 length in hg19
chr2_lengths <- sample(50:200, 50, replace=TRUE)
chr2_ends <- chr2_starts + chr2_lengths
chr2_tms <- runif(50, min=60, max=80)
# Create GRanges object
tm_results <- GRanges(
seqnames = Rle(c(rep("chr1", 100), rep("chr2", 50))),
ranges = IRanges(
start = c(chr1_starts, chr2_starts),
end = c(chr1_ends, chr2_ends)
),
strand = Rle(sample(c("+", "-"), 150, replace=TRUE)),
Tm = c(chr1_tms, chr2_tms)
)
genome(seqinfo(tm_results)) <- "hg38"
# Example usage by plot_tm_karyotype
plot_tm_karyotype(tm_results, genome_assembly = "hg38")
# Example usage by plot_tm_genome_tracks with custom settings (plot_type=4)
plot_tm_karyotype(tm_results,
genome_assembly = "hg38",
plot_type = 4,
xaxis_cex = 0.5
)
# Example usage by plot_tm_genome_tracks with default settings (plot_type=1)
plot_tm_genome_tracks(tm_results, chromosome_to_plot = "chr1", genome_assembly = "hg38")
# Create example GRanges object
gr_tm <- GenomicRanges::GRanges(
seqnames = c("chr1", "chr2", "chr1", "chr2", "chr1"),
ranges = IRanges::IRanges(
start = c(100, 200, 300, 400, 150),
end = c(150, 250, 350, 450, 200)
),
Tm = c(65.5, 68.2, 70.1, 63.8, 72.0)
)
# Plot with ideograms
plot_tm_heatmap(gr_tm, genome_assembly = "hg19", plot_type = "karyogram")
# Faceted plot by chromosome
plot_tm_heatmap(gr_tm, genome_assembly = "hg19", plot_type = "faceted")
launch the shiny application
TmCalculatorShiny::TmCalculator_shiny()
Conclusion
The TmCalculator package provides a comprehensive suite of tools for
calculating and analyzing melting temperatures of DNA/RNA sequences. The
visualization tools help in understanding the genomic context and
comparing Tm values across different sequences.
For more information, please refer to the package documentation and
examples.