get_ase_volcano_plot: Generate a volcano plot for diff. ASE.

In cparsania/parcutils: Utility Functions To Deal Day To Day Bioinformatics Tasks.

Generate a volcano plot for diff. ASE.

Description

Generate a volcano plot for diff. ASE.

Usage

get_ase_volcano_plot(
  x,
  sample_comparison,
  event_type = "IR",
  log2fc_cutoff = 1,
  pval_cutoff = 0.05,
  ASE_to_display = NULL,
  lab_size = 3,
  point_size = 1,
  repair_ASE = TRUE,
  col_up = "#a40000",
  col_down = "#007e2f",
  col_other = "grey",
  facet_event_type = TRUE,
  facte_nrow = NULL,
  facet_ncol = NULL,
  facet_scale = "fixed",
  facet_shrink = TRUE,
  facet_labeller = "label_value",
  facet_as.table = TRUE,
  facet_drop = TRUE,
  facet_dir = "h",
  facet_strip.position = "top",
  ...
)

Arguments

x	an abject of class "parcutils_ase". This is an output of the function run_ase_diff_analysis().
sample_comparison	a character string denoting a valid differential ASE comparison. Possible comparisons can be found from x$de_comparisons.
event_type	a character string, default "IR" denoting valid event_type to display in the volcano plot. Values could be one of the "IR","SE","AFE","ALE","MXE","A3SS","A5SS".
log2fc_cutoff	a numeric value denoting logFC cutoff for volcano plot. Default 1.
pval_cutoff	a numeric value denoting pvalue cutoff for volcano plot. Default 0.05.
ASE_to_display	a character vector of the ASE to display in volcano plot, default NULL, displays non overlapping ASE.
lab_size	a numeric value, default 3, denoting size of the labels.
point_size	a numeric value, default 1, denoting size of the points.
repair_ASE	logical, default TRUE, indicating whether to repair event names. See details.
col_up	a character string, default #a40000, denoting valid color code for up regulated ASE.
col_down	a character string, default #007e2f, denoting valid color code for up regulated ASE.
col_other	a character string, default "grey", denoting valid color code for other than up and down regulated ASE.
facet_event_type	logical, default TRUE, denoting whether to facet plot by event type.
facte_nrow	pass to the argument nrow of ggplot2::facet_wrap().
facet_ncol	pass to the argument ncol of ggplot2::facet_wrap().
facet_scale	pass to the argument scale of ggplot2::facet_wrap().
facet_shrink	pass to the argument shrink of ggplot2::facet_wrap().
facet_labeller	pass to the argument labeller of ggplot2::facet_wrap().
facet_as.table	pass to the argument as.table of ggplot2::facet_wrap().
facet_drop	pass to the argument drop of ggplot2::facet_wrap().
facet_dir	pass to the argument dir of ggplot2::facet_wrap().
facet_strip.position	pass to the argument position of ggplot2::facet_wrap().
...	other parameters to be passed to EnhancedVolcano::EnhancedVolcano().

Details

• repair_ASE: Internally event names are taken from SpliceWiz. When repair_genes is set to TRUE the string corresponding to gene symbol will be extracted. if one gene symbol assinged to more than one events, even names will be used instead of gene symbol (usually the case). This is useful when gene names to be revealed in the volcano plot.

Value

a ggplot2.

Examples

se <- SpliceWiz::SpliceWiz_example_NxtSE(novelSplicing = TRUE)
SpliceWiz::colData(se)$treatment <- rep(c("A", "B"), each = 3)
SpliceWiz::colData(se)$replicate <- rep(c("P","Q","R"), 2)
res <- run_ase_diff_analysis(x = se, test_factor = "treatment", test_nom = "A" ,test_denom = "B",  IRmode ="annotated",  cutoff_lfc = 0.6, cutoff_pval = 1, regul_based_upon = 1)
get_ase_volcano_plot(res,  sample_comparison = res$de_comparisons[1], pval_cutoff = 1) %>% print()

# repair_ASE = FALSE
get_ase_volcano_plot(res,  sample_comparison = res$de_comparisons[1], pval_cutoff = 1,repair_ASE = FALSE) %>% print()

# ASE_to_display = "", don't show any label.
get_ase_volcano_plot(res,  sample_comparison = res$de_comparisons[1], pval_cutoff = 1,ASE_to_display = "") %>% print()

cparsania/parcutils documentation built on Oct. 27, 2024, 4:55 a.m.