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

View source: R/imprints_barplotting_app.R

imprints_barplotting_app

R Documentation

imprints_barplotting_app

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_app(
  data,
  treatmentlevel = get_treat_level(data),
  setlevel = NULL,
  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 = 0.6,
  ret_plot = TRUE,
  save_pdf = FALSE,
  toplabel = "IMPRINTS-CETSA bar plotting",
  leftlabel = "",
  bottomlabel = "",
  pdfname = "barplot",
  pdfheight = 12,
  pdfwidth = 12
)

Arguments

`data`	dataset after imprints_caldiff to plot. Can also be a list of this dataset.
`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
`setlevel`	a vector of set information if any, such as c("M13","M16")
`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

Examples

library(IMPRINTS.CETSA)
library(IMPRINTS.CETSA.app)

elutriation_wVeh <- elutriation[,-grep("G1",names(elutriation))]
O43776_elu <- elutriation_wVeh[which(elutriation_wVeh$id == "O43776"),]
imprints_barplotting_app(O43776_elu)

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