shiftPlots: Plot shifted heatmaps per library

In ORFik: Open Reading Frames in Genomics

Description

A good validation for you p-shifting, to see shifts are corresponding and close to the CDS TIS.

Usage

shiftPlots(
  df,
  output = NULL,
  title = "Ribo-seq",
  scoring = "transcriptNormalized",
  addFracPlot = TRUE,
  BPPARAM = bpparam()
)

Arguments

df	an ORFik experiment
output	name to save file, full path. (Default NULL) No saving.
title	Title for top of plot, default "Ribo-seq". A more informative name could be "Ribo-seq zebrafish Chew et al. 2013"
scoring	which scoring scheme to use for heatmap, default "transcriptNormalized". Some alternatives: "sum", "zscore".
addFracPlot	logical, default TRUE, add positional sum plot on top per heatmap.
BPPARAM	how many cores/threads to use? default: bpparam()

Value

a ggplot2 grob object

Examples

df <- ORFik.template.experiment()
df <- df[3,] #lets only p-shift RFP sample at index 3
#shiftFootprintsByExperiment(df, output_format = "bedo)
#shiftPlots(df, title = "Ribo-seq Human ORFik et al. 2020")

ORFik documentation built on March 27, 2021, 6 p.m.