plot_ma: MA Plot

In zentnerlab/TSRexploreR: TSS and TSR Analysis

MA Plot

Description

Generate an MA plot for differential TSSs or TSRs.

Usage

plot_ma(
  experiment,
  data_type = c("tss", "tsr"),
  de_comparisons = "all",
  ncol = 1,
  log2fc_cutoff = 1,
  fdr_cutoff = 0.05,
  ...
)

Arguments

experiment	TSRexploreR object.
data_type	Whether to plot differential TSSs ('tss') or TSRs ('tsr').
de_comparisons	Character vector of differential expression comparisons to plot.
ncol	Integer specifying the number of columns to arrange multiple plots.
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.
...	Arguments passed to geom_point.

Details

This function generates an MA plot of the results from differential analysis of TSSs or TSRs.

'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 coloring of features as significantly altered in the plot.

Value

ggplot2 object of MA plot.

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=rep(NA, 6), file_2=rep(NA, 6),
  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_ma(diff_tss, data_type="tss")

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