rank_order_scatter: Plot the rank order of the data in two tables against each...
In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

rank_order_scatter

R Documentation

Plot the rank order of the data in two tables against each other.

Description

Steve Christensen has some neat plots showing the relationship between two tables. I thought they were cool, so I co-opted the idea in this function.

Usage

rank_order_scatter(
  first,
  second = NULL,
  first_type = "limma",
  second_type = "limma",
  first_table = NULL,
  alpha = 0.5,
  second_table = NULL,
  first_column = "logFC",
  second_column = "logFC",
  first_p_col = "adj.P.Val",
  second_p_col = "adj.P.Val",
  p_limit = 0.05,
  both_color = "red",
  first_color = "green",
  second_color = "blue",
  no_color = "black"
)

Arguments

`first`	First table of values.
`second`	Second table of values, if null it will use the first.
`first_type`	Assuming this is from all_pairwise(), use this method.
`second_type`	Ibid.
`first_table`	Again, assuming all_pairwise(), use this to choose the table to extract.
`alpha`	How see-through to make the dots?
`second_table`	Ibid.
`first_column`	What column to use to rank-order from the first table?
`second_column`	What column to use to rank-order from the second table?
`first_p_col`	Use this column for pretty colors from the first table.
`second_p_col`	Use this column for pretty colors from the second table.
`p_limit`	A p-value limit for coloring dots.
`both_color`	If both columns are 'significant', use this color.
`first_color`	If only the first column is 'significant', this color.
`second_color`	If the second column is 'significant', this color.
`no_color`	If neither column is 'significant', then this color.