ms_ggplotting_rep: ms_ggplotting_rep

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, particularly for dataset with replicated runs

Usage

ms_ggplotting_rep(
  data,
  legenddata = NULL,
  levelvector = NULL,
  nread = 10,
  withset = FALSE,
  remsinglecondprot = TRUE,
  PSMcutoff = FALSE,
  PSMthreshold = 3,
  fitremout = FALSE,
  ctrlcond = NULL,
  bottomcutoff = 0.4,
  topcutoff = 0.8,
  variancecutoff = FALSE,
  nMAD_var = 2.5,
  simpleAUC = TRUE,
  topasone = TRUE,
  normTop = TRUE,
  dotconnect = FALSE,
  pfdatabase = FALSE,
  printBothName = TRUE,
  printGeneName = FALSE,
  printcount = TRUE,
  annotypos = 0.5,
  annotyinterval = 0.08,
  presetcolor = TRUE,
  extraidtocomplete = NULL,
  plotfitremout = TRUE,
  plotvarremout = TRUE,
  colorpanel = NULL,
  commonlegend = TRUE,
  layout = c(5, 5),
  external = TRUE,
  toplabel = "CETSA data plotting_curve fitting",
  leftlabel = "Non-denatured protein fraction",
  bottomlabel = "Temperature",
  pdfname = "ggplotting.pdf",
  pdfheight = 12,
  pdfwidth = 12,
  returnplots = FALSE
)

Arguments

data	CETSA melt curve dataset to plot
legenddata	dataset used for condition extraction, at least one protein inside this dataset should contains the full set of experiment conditions
levelvector	a vector of conditions, preferably starting with Ctrl conditions
nread	number of reading channels or sample treatements
withset	whether there is set column to perform facet_grid, default set to FALSE
remsinglecondprot	whether orphan proteins to be plotted, default value is TRUE, so to exclude them from plotting
PSMcutoff	whether to apply PSM threshold cutoff on hit selection, default set to FALSE
PSMthreshold	the threshold of averaged PSM numbers to consider protein quantification as reliable, default value is 3
fitremout	whether to segregate the proteins with messy melt curves, default set to FALSE
ctrlcond	if necessary, could used to specify what conditions to be referred as control conditions, for example "Vech"; by default "DMSO","Ctrl" and "Control" have been automatically included as the keyword for control condition
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
variancecutoff	whether to segregate the proteins with large inter-replicate variance
nMAD_var	the number of MADs to set the significance cutoff about variance distribution, default value is 2.5
simpleAUC	whether to perform a simple calculation of AUC, default set to TRUE
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, default set to TRUE
plotfitremout	whether to plot out messy melt curves, default set to TURE
plotvarremout	whether to plot out large inter-replicate variance melt curves, default set to TRUE
colorpanel	a vector of customizable color scheme provided by the user
commonlegend	whether to use one common legend for whole page of plots, default set to TRUE
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_rep(LY_scaled,
  levelvector=c("Ctrl.1", "Ctrl.2", "Treatment.1","Treatment.2"))

## End(Not run)

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