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Plot the ECDF of log2(fold change) between groups

deseq_fc_ecdf.Rd

This functions will take differential expression results as a data.frame and plot the ECDF for the input gene_lists.

The gene sets to plot should be provided as a named list of vectors.

Example:

gene_lists = list("Background" = c("gene1", "gene2"), "Target" = c("gene2", "gene3"))

The output will be saved to a PDF if an output_filename is provided.

Users can define the groups that are to be compared in the statistical test using the null_name and target_name arguments. The names must be found in gene_lists. The factor_order is used to order the groups in the analysis.

This functions returns:

  • $plot: The ECDF plot

  • $stats: The results object

Usage

deseq_fc_ecdf(
  res,
  gene_lists,
  title = "ECDF",
  output_filename = NULL,
  palette = SeedMatchR.palette,
  factor_order = NULL,
  x_lims = c(-1, 1),
  stats_test = c("KS", "Wilcoxen", "Wass", "DTS"),
  alternative = c("greater", "less", "two.sided"),
  null_name = 1,
  target_name = 2,
  height = 5,
  width = 5,
  dpi = 320,
  theme = SeedMatchR.theme
)

Arguments

res

The differential expression results data frame.

gene_lists

A nested list of gene names. Example: gene_lists = list("Background" = background_list, "Target" = target_list)

title

The tile of the plot.

output_filename

If the output filename is provided, then the plot is saved.

palette

Vector of colors to use for your curves.

factor_order

Vector defining the order to use for the legends.

x_lims

The x-axis range limits.

stats_test

The statistical test to use. Options: KS, Wass, Wilcoxen, or DTS.

alternative

The alternative hypothesis to test. Options: greater, less, two.sided.

null_name

The name in the gene.list to use as the null for ECDF plots.

target_name

The name in the gene.list to use as the target for ECDF.

height

Plot height in inches.

width

Plot width in inches.

dpi

The DPI resolution for the figure.

theme

A ggplot2 theme defining plot parameters.

Value

A ggplot object and ECDF statistics.

Examples

if (FALSE) { # interactive()
library(dplyr)

guide.seq = "UUAUAGAGCAAGAACACUGUUUU"

anno.db = load_annotations("rnor7")

# Load test data
get_example_data("sirna")

sirna.data = load_example_data("sirna")

res <- sirna.data$Schlegel_2022_Ttr_D1_30mkg

# Filter DESeq2 results for SeedMatchR
res = filter_res(res, fdr.cutoff=1, fc.cutoff=0, rm.na.log2fc = TRUE)

res = SeedMatchR(res = res, gtf = anno.db$gtf, seqs = anno.db$seqs,
sequence = guide.seq, seed.name = "mer7m8", tx.id.col= FALSE)

# Gene set 1
mer7m8.list = res$gene_id[res$mer7m8 >= 1]

# Gene set 2
background.list = res$gene_id[res$mer7m8 == 0]

ecdf.results = deseq_fc_ecdf(res,
list("Background" = background.list, "mer7m8" = mer7m8.list))
}