plotDistr_RGList: Plot distributions of signals in a RGList object using...

In peterjuv/FunGenPipe: Tools for building function genomics pipelines

Description

Plots distributions for each combination of FUNS, channels and sampleColors. By default, samples are ordered according to the sampleColors (if provided). Colors should be provided as factors with a preset order of levels; the order of colors is determined by the order of levels

Usage

plotDistr_RGList(
  RGList,
  filePath = NULL,
  channels = c("R", "G"),
  FUNS = c(ggplot2::geom_density, ggplot2::geom_boxplot),
  probeTypeVec = NULL,
  probeTypeValue = 0,
  numProbes = NULL,
  sampleColors = NULL,
  orderByColors = TRUE,
  scale_x_limits = NULL,
  width = 16/9 * 7,
  height = 7,
  ...
)

Arguments

RGList	A list of matrices of signal intensities per channel
filePath	NULL or character; if given, output a PDF; default NULL
channels	List of data.frames from RGList, e.g. list("log2(R)", "log2(G)")
FUNS	geom_functions from ggplot2, default c(geom_density, geom_boxplot), others: c(geom_violin, geom_histogram, ggridges::geom_density_ridges)
probeTypeVec	Vector of probe types
probeTypeValue	Value from probeTypeVec to use for plotting
numProbes	Number of randomly select probes
sampleColors	Tibble of named factors of colors with names matching sample names
orderByColors	Logical for ordering samples by colors (coded as a factor with levels in order); default TRUE
scale_x_limits	NULL for auto-scale; use c(0,16) or less for log2(intensities)
width	PDF width, default 16/9*7=12.44
height	PDF height, default 7
...	Passed to ggplot2::FUN, e.g.: bins, binwidth, show.legend

Value

A list of ggplots, one per a combination of FUNS, channels and sampleColors PDF if filePath is not NULL

Implementation

See https://www.tidyverse.org/blog/2020/02/glue-strings-and-tidy-eval/ for bracing variables. Evaluation of expression: https://adv-r.hadley.nz/evaluation.html. For bquote(a +. (b)): http://adv-r.had.co.nz/Expressions.html.

Examples

## Not run: 
plotDistr_RGList(dataRG.bgc, file.path(curDir, "density-boxplot_dataRG.bgc_genes.pdf"), 
channels = c("log2R","log2G","beta"), probeTypeVec = dataRG.bgc$genes$ControlType, probeTypeValue = 0,
numProbes = 10000, sampleColors = targets %>% select(starts_with("color_")))
## Removed parameters/code:
# transform = log2: transformation function applied to each channel (default: log2; identity for none)
mutate("{{transform}}({ch})" := transform(!!parse_expr(ch)))
ggplot(aes(x=transform(!!parse_expr(ch)), color=HybName)) +
ggplot(d2, aes(x=!!parse_expr(ch), color=fct_reorder(HybName, order(colors)))) + #, order=colors)) + 

## End(Not run)

peterjuv/FunGenPipe documentation built on June 18, 2021, 3:38 a.m.