imprints_plotting_isoform_peptides: imprints_plotting_isoform_peptides

In mgerault/mineCETSAapp: A shiny app for IMPRINTS.CETSA package

imprints_plotting_isoform_peptides

Description

Function to visualize the isoform sequence alignment with its canonical form obtained from the function imprints_isoform_peptides to compare with the cleavage site obtained by imprints_cleaved_peptides.

Usage

imprints_plotting_isoform_peptides(
  data,
  data_isoform,
  control,
  treatment,
  min_ValidValue = 0.4,
  ret_plot = TRUE,
  save_pdf = FALSE,
  layout = c(1, 2),
  toplabel = "",
  leftlabel = "",
  bottomlabel = "",
  pdfname = "isoform_alignement_plots",
  pdfheight = 9,
  pdfwidth = 18
)

Arguments

data	The normalized peptides data set, i.e. the outpout from imprints_normalize_peptides.
data_isoform	The cleavage hits data aligned with the potential isoforms, i.e. the outpout from imprints_isoform_peptides.
control	The control treatment from your dataset.
treatment	The treatment from which you want to see the peptides fold-changes. Can only be one.
min_ValidValue	The minimum proportion of non-missing values per peptides. Default is 0.4; so if 6 temperatures need at least 3 non missing values.
ret_plot	Logical to tell if you want to return the last plot
save_pdf	A logical to tell if you want to save plots in a pdf file
layout	A vector indicating the panel layout for multi-panel plots per page, default value is c(2,2), use when save_pdf = TRUE
toplabel	textual label at the top part of the page
leftlabel	textual label at the left side of the page
bottomlabel	textual label at the bottom part of the page
pdfname	Character to label the pdf file
pdfheight	Numeric indicating the height of pdf file, default value 12
pdfwidth	Numeric indicating the width of pdf file, default value 12

Details

The plot will show you how each peptides aligns with the canonical sequence. Each peptide will be clustered in two groups, the one with greatest log2 fold-change and the ones with the lowest. This has been thought for a final control of the results from imprints_isoform_peptides and imprints_cleaved_peptides in order to see if a protein having a significant RESP effect could be due to the expression of an alternative splicing form.

Value

The plots of the isoform sequence alignment

See Also

imprints_isoform_peptides

mgerault/mineCETSAapp documentation built on April 17, 2025, 7:24 p.m.