ms_ggplotting: ms_ggplotting

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

Description

Function to generate pdf files with multipanel ggplots for melt curve data

Usage

ms_ggplotting(
  data,
  legenddata = NULL,
  nread = 10,
  remsinglecondprot = TRUE,
  fitremout = FALSE,
  ctrlcond = NULL,
  bottomcutoff = 0.4,
  topcutoff = 0.8,
  orderAUCdiff = TRUE,
  simpleAUC = TRUE,
  nreplicate = 1,
  topasone = TRUE,
  normTop = TRUE,
  dotconnect = FALSE,
  pfdatabase = FALSE,
  printBothName = TRUE,
  printGeneName = FALSE,
  printcount = TRUE,
  annotypos = 0.5,
  annotyinterval = 0.08,
  presetcolor = TRUE,
  colorpanel = NULL,
  extraidtocomplete = NULL,
  plotfitremout = TRUE,
  withset = FALSE,
  commonlegend = TRUE,
  layout = c(5, 5),
  external = TRUE,
  toplabel = "CETSA data plotting_curve fitting",
  leftlabel = "Non-denatured protein fraction",
  bottomlabel = "Temperature",
  returnplots = FALSE,
  pdfname = "ggplotting.pdf",
  pdfheight = 12,
  pdfwidth = 12
)

Arguments

data	isothermal dataset to plot
legenddata	dataset used for condition extraction, at least one protein inside this dataset should contains the full set of experiment conditions
nread	number of reading channels or sample treatements
remsinglecondprot	whether orphan proteins to be plotted, default value is TRUE, soto exclude them from plotting
fitremout	whether to segregate the proteins with messy melt curves
ctrlcond	if necessary, could used to specify what conditions to be referred as control conditions, Ctrl/Control/DMSO is included as default keyword
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
orderAUCdiff	whether to order plots by AUC difference among different treatment for same protein, default set to TRUE
simpleAUC	whether to perform a simple calculation of AUC, default set to TRUE
nreplicate	number of replicates, default value is 1
topasone	whether the top plateau has to be fixed, i.e., 1.0
normTop	whether to normalize the AUC based on Top three readings
dotconnect	whether to simply dot connect the readings for each curve
printcount	whether to annotate the plots with PSM and uniPeptide number
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
presetcolor	whether to use the pre-defined color scheme
colorpanel	a vector of customizable color scheme provided by the user
plotfitremout	whether to plot out messy melt curves
commonlegend	whether to use one common legend for whole page of plots
layout	a vector indicating the panel layout for multi-panel plots per page
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(LY_scaled)

## End(Not run)

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