transcriptWindow1 {ORFik} | R Documentation |
Given as single window
transcriptWindow1( df, outdir = NULL, scores = c("sum", "zscore"), colors = experiment.colors(df), title = "Coverage metaplot", windowSize = 100, returnPlot = is.null(outdir), dfr = NULL, idName = "", format = ".png", type = "ofst", BPPARAM = bpparam() )
df |
an ORFik |
outdir |
directory to save to (default: NULL, no saving) |
scores |
scoring function (default: c("sum", "zscore")), see ?coverageScorings for possible scores. |
colors |
Which colors to use, default auto color from function
|
title |
title of ggplot |
windowSize |
size of binned windows, default: 100 |
returnPlot |
return plot from function, default is.null(outdir), so TRUE if outdir is not defined. |
dfr |
an ORFik |
idName |
A character ID to add to saved name of plot, if you make several plots in the same folder, and same experiment, like splitting transcripts in two groups like targets / nontargets etc. (default: "") |
format |
default (".png"), do ".pdf" if you want as pdf |
type |
a character(default: "bedoc"), load files in experiment or some precomputed variant, either "bedo", "bedoc", "pshifted" or default. These are made with ORFik:::simpleLibs(), shiftFootprintsByExperiment().. Will load default if bedoc is not found |
BPPARAM |
how many cores/threads to use? default: bpparam() |
NULL, or ggplot object if returnPlot is TRUE
Other experiment plots:
transcriptWindowPer()
,
transcriptWindow()