te.plot {ORFik} | R Documentation

## 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 = paste0(dirname(df.rfp$filepath[1]), "/QC_STATS/"),
      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)

[Package ORFik version 1.12.13 Index]