ma_plot: Bland-Altman plot
In bryancquach/omixjutsu: Utilities for omics analysis tasks

ma_plot.DESeqResults

R Documentation

Bland-Altman plot

Description

Plot log fold changes vs. log expression level.

Usage

## S3 method for class 'DESeqResults'
ma_plot(
  dds_results,
  outliers = NULL,
  sig_cutoff = 0.05,
  sig_up_color = "red4",
  sig_down_color = "steelblue3",
  nonsig_color = "gray60",
  outlier_color = "goldenrod3",
  sig_alpha = 0.8,
  nonsig_alpha = 0.4,
  sig_size = 3,
  nonsig_size = 2,
  outlier_size = sig_size * 2.5
)

ma_plot(object, ...)

## S3 method for class 'data.frame'
ma_plot(
  data,
  basemean_colname,
  fc_colname,
  adj_pvalue_colname,
  outlier_index = NULL,
  sig_cutoff = 0.05,
  sig_up_color = "red4",
  sig_down_color = "steelblue3",
  nonsig_color = "gray60",
  outlier_color = "goldenrod3",
  sig_alpha = 0.8,
  nonsig_alpha = 0.4,
  sig_size = 3,
  nonsig_size = 2,
  outlier_size = sig_size * 2.5
)

Arguments

`outliers`	A vector of outlier IDs.
`sig_cutoff`	Adjusted p-value significance threshold.
`sig_up_color`	Point color for statistically significant up-regulated features.
`sig_down_color`	Point color for statistically significant down-regulated features.
`nonsig_color`	Point color for features not statistical significant.
`outlier_color`	Point color for statistically significant features flagged as outliers.
`sig_alpha`	Point color alpha value for statistically significant features.
`nonsig_alpha`	Point color alpha value for features not statistically significant.
`sig_size`	Point size value for statistically significant features.
`nonsig_size`	Point size value for outliers.
`object`	A DESeqResults or data.frame object.
`basemean_colname`	A string denoting the column in `data` that contains the base mean expression values.
`fc_colname`	A string denoting the column in `data` that contains the log2 fold changes.
`adj_pvalue_colname`	A string denoting the column in `data` that contains the adjusted p-values.
`outlier_index`	A numeric vector denoting row indices of outliers.