te.plot: Translational efficiency plots

In JokingHero/ORFik: Open Reading Frames in Genomics

Translational efficiency plots

Description

Create 2 TE plots of:
- Within sample (TE log2 vs mRNA fpkm) ("default")
- Between all combinations of samples (x-axis: rna1fpkm - rna2fpkm, y-axis rfp1fpkm - rfp2fpkm)

Usage

te.plot(
  df.rfp,
  df.rna,
  output.dir = QCfolder(df.rfp),
  type = c("default", "between"),
  filter.rfp = 1,
  filter.rna = 1,
  collapse = FALSE,
  plot.title = "",
  plot.ext = ".pdf",
  width = 6,
  height = "auto"
)

Arguments

df.rfp	a experiment of Ribo-seq or 80S from TCP-seq.
df.rna	a experiment of RNA-seq
output.dir	directory to save plots, plots will be named "TE_between.pdf" and "TE_within.pdf"
type	which plots to make, default: c("default", "between"). Both plots.
filter.rfp	numeric, default 1. minimum fpkm value to be included in plots
filter.rna	numeric, default 1. minimum fpkm value to be included in plots
collapse	a logical/character (default FALSE), if TRUE all samples within the group SAMPLE will be collapsed to one. If "all", all groups will be merged into 1 column called merged_all. Collapse is defined as rowSum(elements_per_group) / ncol(elements_per_group)
plot.title	title for plots, usually name of experiment etc
plot.ext	character, default: ".pdf". Alternatives: ".png" or ".jpg".
width	numeric, default 6 (in inches)
height	numeric or character, default "auto", which is: 3 + (ncol(RFP_CDS_FPKM)-2). Else a numeric value of height (in inches)

Details

Ribo-seq and RNA-seq must have equal nrows, with matching samples. Only exception is if RNA-seq is 1 single sample. Then it will use that for each of the Ribo-seq samples. Same stages, conditions etc, with a unique pairing 1 to 1. If not you can run collapse = "all". It will then merge all and do combined of all RNA-seq vs all Ribo-seq

Value

a data.table with TE values, fpkm and log fpkm values, library samples melted into rows with split variable called "variable".

Examples

##
# df.rfp <- read.experiment("zf_baz14_RFP")
# df.rna <- read.experiment("zf_baz14_RNA")
# te.plot(df.rfp, df.rna)
## Collapse replicates:
# te.plot(df.rfp, df.rna, collapse = TRUE)

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.