draw_value_idr_scatterplot: Create scatterplot of IDR values

In kkrismer/idr2d: Irreproducible Discovery Rate for Genomic Interactions Data

Create scatterplot of IDR values

Description

Creates diagnostic plots to visualize the results of estimate_idr.

Usage

draw_value_idr_scatterplot(
  df,
  remove_na = TRUE,
  remove_outliers = TRUE,
  xlab = "transformed value in replicate 1",
  ylab = "transformed value in replicate 2",
  log_axes = FALSE,
  log_idr = FALSE,
  title = "value - 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: value numeric; p-value, FDR, or heuristic used to rank the peaks rep_value numeric; value 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?
remove_outliers	logical; removes extreme data points
xlab	character; x axis label
ylab	character; y axis label
log_axes	logical; show logarithmized values from replicate 1 and 2 (default value is FALSE)
log_idr	logical; use logarithmized IDRs for colors to better distinguish highly significant IDRs (default value is FALSE)
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 value scatterplot

Examples

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

kkrismer/idr2d documentation built on Feb. 7, 2024, 2:23 p.m.