draw_value_idr_scatterplot: Create scatterplot of IDR values

View source: R/visualization.R

draw_value_idr_scatterplotR Documentation

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.