plot_shift_rank.RdBarplot of shift scores ranked by score.
plot_shift_rank( experiment, samples = "all", score_order = "descending", ncol = 3 )
| experiment | TSRexploreR object. |
|---|---|
| samples | A vector of sample names to analyze. |
| score_order | Either 'descending' or 'ascending'. |
| ncol | Integer specifying the number of columns to arrange multiple plots. |
ggplot2 object of ranked shifting scores.
The 'tss_shifting' function uses the earth mover's score (EMS) to assess shifts in TSS distribution in consensus TSRs between two samples. This function generates a barplot of shifting scores, with the x-axis corresponding to TSS clusters ordered by tss shifting score, and the y-axis the shifting score. TSRs can be in ascending or descending order as controlled by 'score_order'.
tss_shift to calculate TSS cluster shifting.
data(TSSs) assembly <- system.file("extdata", "S288C_Assembly.fasta", package = "TSRexploreR") samples <- data.frame( sample_name=c(sprintf("S288C_D_%s", seq_len(3)), sprintf("S288C_WT_%s", seq_len(3))), file_1=rep(NA, 6), file_2=rep(NA, 6), condition=c(rep("Diamide", 3), rep("Untreated", 3)) ) exp <- TSSs %>% tsr_explorer(sample_sheet=samples, genome_assembly=assembly) %>% format_counts(data_type="tss") %>% tss_clustering(threshold=3) %>% merge_samples(data_type="tss", merge_group="condition") %>% merge_samples(data_type="tsr", merge_group="condition") %>% tss_shift( sample_1=c(TSS="S288C_WT_1", TSR="S288C_WT_1"), sample_2=c(TSS="S288C_D_1", TSR="S288C_D_1"), comparison_name="Untreated_vs_Diamide", max_distance = 100, min_threshold = 10, n_resamples = 1000L )#> Warning: Arguments in '...' ignored#> Warning: Arguments in '...' ignored#> Warning: Arguments in '...' ignored#> Warning: Arguments in '...' ignored#> Warning: Arguments in '...' ignored#> Warning: Arguments in '...' ignored#> Warning: Arguments in '...' ignored#> Warning: Arguments in '...' ignored#> Warning: Arguments in '...' ignored#> Warning: Arguments in '...' ignored#> Warning: Arguments in '...' ignored#> Warning: Arguments in '...' ignored#> Warning: Arguments in '...' ignored#> Warning: Arguments in '...' ignored#> Warning: Arguments in '...' ignored#> Warning: Some sequences have fewer than nthresh scores for at least one sample. #> These are ignored and returned as NA.#>p <- plot_shift_rank(exp)