plot_num_de: Plot DE Numbers

In zentnerlab/TSRexploreR: TSS and TSR Analysis

Plot DE Numbers

Description

Stacked barplot of the number of differential TSSs or TSRs per comparison.

Usage

plot_num_de(
  experiment,
  data_type = c("tss", "tsr"),
  de_comparisons = "all",
  log2fc_cutoff = 1,
  fdr_cutoff = 0.05,
  keep_unchanged = FALSE,
  return_table = FALSE,
  ...
)

Arguments

experiment	TSRexploreR object.
data_type	Whether to plot numbers of differential TSSs ('tss') or TSRs ('tsr').
de_comparisons	Character vector of differential expression comparisons to plot.
log2fc_cutoff	Differential features not meeting this |log2(fold change)| threshold will not be considered.
fdr_cutoff	Differential features not meeting this significance threshold will not be considered.
keep_unchanged	Whether to include (TRUE) unchanged features in the plot.
return_table	Return a table of results instead of a plot.
...	Additional arguments passed to geom_col.

Details

Generate a stacked barplot with the number of differential TSSs or TSRs per comparison.

'de_comparisons' are the names given to the comparisons from the 'comparison_name' argument of the 'differential_expression' function. 'log2fc_cutoff' and 'fdr_cutoff' are the log2(fold change) and FDR cutoffs used for determination of significance in the plot. 'keep_unchanged' controls whether non-significant feature numbers are included in the plot.

If 'keep_unchanged' is TRUE, a table with the numbers is returned instead of the ggplot. This may be useful if the exact numbers underlying the plot are required.

Value

ggplot2 object of stacked barplot. If 'return_table' is TRUE, a data.frame with differentially expressed TSS/TSR numbers are returned.

See Also

fit_de_model to fit a differential expression model. differential_expression to find differential TSSs or TSRs.

Examples

data(TSSs)
sample_sheet <- data.frame(
  sample_name=c(
    sprintf("S288C_D_%s", seq_len(3)),
    sprintf("S288C_WT_%s", seq_len(3))
  ),
  file_1=NA, file_2=NA,
  condition=c(rep("Diamide", 3), rep("Untreated", 3))
)

exp <- TSSs %>%
  tsr_explorer(sample_sheet=sample_sheet) %>%
  format_counts(data_type="tss")

diff_tss <- exp %>%
  fit_de_model(data_type="tss", formula= ~condition, method="edgeR") %>%
  differential_expression(
  data_type="tss", 
  comparison_name="Diamide_vs_Untreated",
  comparison_type="coef",
  comparison=2)
  
p <- plot_num_de(diff_tss, data_type="tss")

zentnerlab/TSRexploreR documentation built on Dec. 30, 2022, 10:27 p.m.