ms_ggplotting_errorbar: ms_ggplotting_errorbar

In nkdailingyun/mineCETSA: Processing and Visualization of Proteome-wide MS-CETSA data

Description

Function to generate pdf files with multipanel ggplots for replicated (ideally at least three) CETSA melt curve data, in the format of a mean +/- errorbar

Usage

ms_ggplotting_errorbar(
  data,
  extradata = NULL,
  legenddata = NULL,
  levelvector = NULL,
  nread = 10,
  minireplicate = NULL,
  witherrorbar = TRUE,
  fitremout = FALSE,
  bottomcutoff = 0.4,
  topcutoff = 0.8,
  topasone = TRUE,
  pfdatabase = FALSE,
  keepcommonprotein = TRUE,
  printBothName = TRUE,
  printGeneName = FALSE,
  printcount = TRUE,
  printTm = TRUE,
  annotypos = 0.5,
  annotyinterval = 0.08,
  layout = c(5, 5),
  external = TRUE,
  withpoints = TRUE,
  presetcolor = TRUE,
  colorpanel = NULL,
  nshape = 5,
  nsize = 2,
  toplabel = "CETSA data plotting_error bar",
  leftlabel = "Non-denatured protein fraction",
  bottomlabel = "Temperature",
  returnplots = FALSE,
  pdfname = "ggplotting.pdf",
  pdfheight = 12,
  pdfwidth = 12
)

Arguments

data	dataset to plot, ideally with the fitting information but not complusory
extradata	dataset with extrapolated readings, default to NULL
legenddata	dataset used for condition extraction, at least one protein inside this dataset should contains the full set of experiment conditions, most of the time there is no need to supply, just use the data instead
levelvector	a vector of experimental conditions
nread	number of reading channels or sample treatements
minireplicate	ideally at least three replicates of measurments for the same proteins are required to plot in a box plot format
witherrorbar	whether to plot in a mean +/- error bar(se) graph format, default to TRUE
fitremout	whether to segregate the proteins with messy melt curves, default set to FALSE
bottomcutoff	the average of the last three points should be lower than specified bottom cutoff value, which is 0.4 by default
topcutoff	the average of the first three points should be higher than specified bottom cutoff value, which is 0.8 by default
topasone	whether the top plateau has to be fixed, i.e., 1.0
keepcommonprotein	whether to only keep the proteins also present in the provided extradata set, default set to TRUE
printTm	whether to annotate the plots with Tm values, however in this version, when there is more than one sample or no replicates, the Tm annotation would be switched off
annotypos	the starting y-axis position of textual annotation, default value 0.5
annotyinterval	the interval on y-axis for textual annotation, default valule 0.08
layout	a vector indicating the panel layout for multi-panel plots per page
withpoints	whether to fit curve with the reading points, default set to TRUE
presetcolor	whether to use the pre-defined color scheme
colorpanel	a vector of customizable color scheme provided by the user
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	name for the pdf plots 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

a list of ggplot2 object

Examples

## Not run: 
ms_ggplotting_errorbar(LY_fitted)

## End(Not run)

nkdailingyun/mineCETSA documentation built on Feb. 27, 2021, 8:26 p.m.