draw_rank_idr_scatterplot: Create scatterplot of IDR values

In idr2d: Irreproducible Discovery Rate for Genomic Interactions Data

Description

Creates diagnostic plots to visualize the results of estimate_idr.

Usage

draw_rank_idr_scatterplot(
  df,
  remove_na = TRUE,
  xlab = "rank in replicate 1",
  ylab = "rank in replicate 2",
  log_idr = FALSE,
  title = "rank - IDR dependence",
  color_gradient = c("rainbow", "default"),
  alpha = 1,
  max_points_shown = 2500
)

Arguments

df	part of output of estimate_idr, a data frame with at least the following named columns: rank integer; rank of the peak, established by value column, ascending order rep_rank integer; rank of corresponding replicate peak. idr IDR of the peak and the corresponding peak in the other replicate.
remove_na	logical; should NA values be removed?
xlab	character; x axis label
ylab	character; y axis label
log_idr	logical; use logarithmized IDRs for colors to better distinguish highly significant IDRs
title	character; plot title
color_gradient	character; either "rainbow" or "default"
alpha	numeric; transparency of dots, from 0.0 - 1.0, where 1.0 is completely opaque; default is 1.0
max_points_shown	integer; default is 2500

Value

ggplot2 object; IDR rank scatterplot

Examples

idr_results <- estimate_idr1d(idr2d:::chipseq$rep1_df,
                              idr2d:::chipseq$rep2_df,
                              value_transformation = "log")
draw_rank_idr_scatterplot(idr_results$rep1_df)

idr2d documentation built on Nov. 8, 2020, 6:16 p.m.