compare_replicates: Correlation plots for numeric data

In lakhanp1/chipmine: Analyze ChIP-seq Data

Description

Correlation plots for numeric data

Usage

compare_replicates(
  data,
  rep1Col,
  rep2Col,
  value = "FPKM",
  trans = "identity",
  pseudoCount = 0
)

Arguments

data	A dataframe
rep1Col	column name for replicate 1
rep2Col	column name for replicate 1
value	A character name for the value. Default: FPKM
trans	trans argument from ggplot::scale_x_continuous() function.
pseudoCount	A pseudo count to avoid log(0) = Inf error. All values less than this number will be set to this number in XY scatter plot. Default: 0

Value

A list with following elements is returned.

• data: plot data used for plotting

• figure: A combined figure generated by ggpubr::ggarrange

• plots: Individual ggplot list for each plot.

  • table: a ggtable object for quantile stats

  • density: a FPKM density plot for both replicates

  • scatter: A list with two scatter plot objects: value, rank

  • corrVariation: A line plot showing changing correlation with quantile subset of data.

Examples

NA

lakhanp1/chipmine documentation built on March 6, 2021, 9:06 a.m.