Plot statistic of significant differential sites between experimental condition returned by the res.pv function

Usage

plot_stat(
  ribo = ribo,
  plot_all = FALSE,
  cscore_cutoff = 0.05,
  adjust_pvalues_method = "fdr",
  site = NULL,
  compute_pval = compute_pval,
  pthr = 0.05,
  condition_col = NULL
)

Arguments

ribo: a RiboClass
plot_all: a logical set to FALSE to plot only significants sites and TRUE to plot all sites
cscore_cutoff: cutoff of c-score under which sites are not taken in account
adjust_pvalues_method: Method to adjust p-value
site: sites to plot
compute_pval: df of p values extracted from compute_pval.R
pthr: p value threshold under which sites are not taken in account
condition_col: the condition column used for calculation in metadata

Value

a ggplot object

Examples

data("ribo_toy")
data("human_methylated")
ribo_toy <- remove_ribo_samples(ribo_toy,c("RNA1", "RNA2"))
ribo_toy <- rename_rna(ribo_toy)  
ribo_toy <- annotate_site(ribo_toy,
                                annot = human_methylated,
                                anno_rna = "rRNA",
                                anno_pos = "Position",
                                anno_value = "Nomenclature")
compute_pval <- compute_pval(ribo = ribo_toy, test = "kruskal", condition_col = "condition") 
plot_stat(ribo = ribo_toy, site = NULL, compute_pval = compute_pval, pthr = 0.05, 
condition_col = "condition", cscore_cutoff = 0.05)
#> Warning: filter on p_adj