imprints_barplotting_simprof: imprints_barplotting_simprof

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

imprints_barplotting_simprof

Description

Function to generate IMPRINTS bar plot and pdf file with multipanel bar plots for IMPRINTS-CETSA data of proteins which have similar profile from a selected protein.

Usage

imprints_barplotting_simprof(
  data,
  data_average = NULL,
  treatmentlevel = "Buparlisib6h",
  protein_profile = "P85037",
  setlevel = NULL,
  printBothName = TRUE,
  printGeneName = FALSE,
  score_threshold = 0.9,
  max_na_prow = 0,
  use_score = "euclidean",
  witherrorbar = TRUE,
  layout = NULL,
  colorpanel = "#18FF00",
  usegradient = FALSE,
  colorgradient = c("#4575B4", "ivory", "#D73027"),
  linegraph = FALSE,
  log2scale = TRUE,
  ratio = 0.6,
  ret_plot = FALSE,
  withpopup = FALSE,
  continue = TRUE,
  modvar = "",
  got_it = FALSE,
  save_prlist = TRUE,
  save_pdf = TRUE,
  toplabel = "IMPRINTS-CETSA bar plotting",
  leftlabel = "",
  bottomlabel = "",
  pdfname = "barplot",
  pdfheight = 12,
  pdfwidth = 12
)

Arguments

data	Dataset after imprints_caldiff to plot.
data_average	Dataset after imprints_average. If null, will get it from data.
treatmentlevel	A single character element which corresponds to one of the condition from the data
protein_profile	A single character element which corresponds to one of the protein from the data that you want the similar profile
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
score_threshold	A numeric value to indicate the threshold, default set to 0.9
max_na_prow	An integer indicating the maximum number of missing value for one protein
use_score	A single character element that define the method score. Method available : 'euclidean' or 'pearson'
witherrorbar	A logical to print or not the error bar on the plot
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 bar plot from the protein selected
withpopup	A logical, only use in shiny context. If TRUE, will call a modal dialog in a shiny app; else, it will ask a question directly in the R console (readline function)
continue	A logical to tell if you wanna continue and get the bar plots after getting the similar profile. This was thought when withpopup is TRUE. If continue is FALSE will only stop after getting similar profiles.
modvar	A character used when withpopup is TRUE, so in shiny context. Y or YES and the function goes on; N or NO and the function stop (doesn't save and return the similar protein profiles)
got_it	A logical to tell if you already have your data filtered. If TRUE, will directly starting to get the bar plot.
save_prlist	A logical to tell if you want to save or not the protein list with a similar profile
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 similar barplots

See Also

imprints_barplotting_app , imprints_corr_to_ref

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