imprints_barplotting_peptides: imprints_barplotting_peptides

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

imprints_barplotting_peptides

Description

Function to generate IMPRINTS bar plot and pdf file with multipanel bar plots for IMPRINTS-CETSA data. This function is based on the function imprints_barplotting from the IMPRINTS.CETSA package.

Usage

imprints_barplotting_peptides(
  data,
  treatmentlevel = get_treat_level(data),
  RESP = FALSE,
  printBothName = TRUE,
  printGeneName = FALSE,
  witherrorbar = TRUE,
  withpoint = FALSE,
  pointperrep = TRUE,
  layout = NULL,
  colorpanel = PaletteWithoutGrey(treatmentlevel),
  usegradient = FALSE,
  colorgradient = c("#4575B4", "ivory", "#D73027"),
  linegraph = FALSE,
  log2scale = TRUE,
  ratio = 1.2,
  ret_plot = TRUE,
  save_pdf = FALSE,
  toplabel = "IMPRINTS-CETSA bar plotting",
  leftlabel = "",
  bottomlabel = "",
  pdfname = "barplot",
  pdfheight = 12,
  pdfwidth = 12
)

Arguments

data	dataset after imprints_sequence_peptides to plot.
treatmentlevel	a vector of treatment labels, such as c("DMSO","TNFa","AT26533") the order determines the arrangement, so in this case DMSO group would be the first group
RESP	Logical to tell if you want to plot IMPRINTS profile in the RESP format (imprints_cleaved_peptides). In order to be able to do it, you'll need exactly 2 peptide sequence per protein.
printBothName	A logical to tell if you want to print the both protein names on the plot
printGeneName	A logical to tell if you want to print the gene names on the plot
witherrorbar	A logical to print or not the error bar on the plot
withpoint	A logical to print or not the data point of each replicate on the plot on top of the bars
pointperrep	A logical to separate the point per replicate; only active when withpoint is set to TRUE
layout	a vector indicating the panel layout for multi-panel plots per page, default value is c(2,3) for set containing data, otherwise c(4,3), use when save_pdf = TRUE
colorpanel	a vector of color scheme provided by default with the function PaletteWithoutGrey
usegradient	whether the barplot should be draw in color gradient format
colorgradient	the color scheme of gradient applied, default value c("#4575B4","ivory", "#D73027")
linegraph	whether to plot the graph in a line graph format, default set to FALSE
log2scale	whether the yscales should be in log2 scale, default set to TRUE
ratio	aspect ratio of the plot, default set to 0.6
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
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	textual label of the pdf file
pdfheight	a number indicate the height of pdf file, default value 12
pdfwidth	a number indicate the width of pdf file, default value 12

Value

The imprints barplot

See Also

imprints_barplotting_app

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