highlights: highlight genes

In olobiolo/siscreenr: Analyze Genome-Wide siRNA Screening Campaigns

Description

Highlight selected genes on a scatter plot of all screen data.

Usage

highlight_genes(
  canvas,
  data,
  genes,
  x.variable,
  y.variable,
  color.points = "lightyellow",
  color.highlight = "purple",
  plot.title = ""
)

color_sections(
  x.treshold = c(-2, 2),
  y.treshold = c(-2, 2),
  outer.limit = 100,
  categories = c("non-hit", "negative interaction", "positive interaction",
    "doubtful viability"),
  category.layout = matrix(c(4, 4, 4, 2, 1, 3, 2, 1, 3), nrow = 3, ncol = 3),
  colpal = c("steelblue1", "springgreen2", "indianred2", "grey85")
)

Arguments

canvas	ggplot object produced by color_sections
data	a data.frame
genes	a character vector of gene symbols to highlight
x.variable, y.variable	names of variables to plot, given as character strings
color.points	color to use for non-highlighted genes
color.highlight	color to use for highlighted genes
plot.title	character string passed to link[ggplot2]{ggtitle}
x.treshold, y.treshold, outer.limit	coordinates that determine section borders x.treshold and y.treshold may be determined as numeric vectors of length one or two
categories	names for sections, in order to appear in the plot legend
category.layout	matrix that maps categories to sections; numbers refer to categories
colpal	colors to assign to sections, in the same order as categories

Details

Given a screen object (a data.frame), produce a scatter plot of two variables. The background is divided into sections with colors signifying the hit status of respective plot regions. Selected points (genes) are plotted with a different color and their gene symbols are added as text labels.

Only sample wells will be plotted.

Value

a ggplot object

a ggplot object with geom_polygon applied

Functions

• highlight_genes: creates scatter plot on colored background

• color_sections: colors sections of the plot background according to hit class

olobiolo/siscreenr documentation built on Nov. 26, 2021, 3:08 p.m.