draw_value_idr_scatterplot {idr2d} | R 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)

[Package idr2d version 1.8.1 Index]