ms_ITTR_ggplotting: ms_ITTR_ggplotting

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

Description

Function to generate pdf files with multipanel ggplots for ITTR data

Usage

ms_ITTR_ggplotting(
  data,
  legenddata = NULL,
  levelvector = NULL,
  nread = 10,
  remsinglecondprot = TRUE,
  robustfitting = FALSE,
  PSMcutoff = FALSE,
  PSMthreshold = 3,
  minireplicate = NULL,
  withset = FALSE,
  orderET = FALSE,
  orderAUC = FALSE,
  simpleAUC = TRUE,
  orderRep = FALSE,
  plotseq = NULL,
  barplotformat = FALSE,
  witherrorbar = FALSE,
  usegradient = TRUE,
  loess = FALSE,
  dotconnect = FALSE,
  pfdatabase = FALSE,
  printBothName = TRUE,
  printGeneName = FALSE,
  unit = "min",
  xtransform = c("xsqrt", "xcubert", "xlog10", "xlog2", "xlinear"),
  xinterval = NULL,
  layout = c(5, 5),
  presetcolor = TRUE,
  colorpanel = NULL,
  toplabel = "ITTR CETSA data plotting",
  bottomlabel = NULL,
  leftlabel = "Non-denatured protein fraction",
  shadearea = NULL,
  shadeoutlinecolor = "black",
  shadefillcolor = "gray90",
  pdfname = "ITTR_ggplotting.pdf",
  external = TRUE,
  pdfheight = 12,
  pdfwidth = 12,
  returnplots = FALSE
)

Arguments

data	ITTR dataset to plot
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, not complusory for isothermal functions
nread	number of reading channels or sample treatements, default value 10
remsinglecondprot	whether orphan proteins to be plotted, default to exclude them from plotting
robustfitting	whether to apply robust fitting, which is new since v.0.3.7
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
minireplicate	number of replicates to keep in final data, default set to NULL, this is an added-on feature to subset enough replicated samples especially for the format with error bar option as discussed below
withset	whether there is set column to perform facet_grid, note that in current version, this argument does not work for the line plot
orderET	whether to order the plots based on ET (Effective concentration)
orderAUC	whether to order the plots based on AUC (Area Under the Curve)
simpleAUC	whether to perform a simple calculation of AUC, default set to TRUE
orderRep	whether to order the plots based on the measurement replicate numbers
plotseq	a vector of plots arragement sequence (composite ID)
barplotformat	whether to plot in a bar graph format, default to FALSE
witherrorbar	whether to plot in a mean +/- errorbar(se) graph format, default to FALSE
loess	whether to perform curve fitting using loess model, default to FALSE
dotconnect	whether to simply dot connect the readings for each curve, default to FALSE
pfdatabase	whether it is Plasmodium falciparum dataset, default to FALSE
printBothName	whether to print both Protein and Gene names, default to TRUE
printGeneName	whether to print only Gene names, default to FALSE, when both printBothName and printBothName are FALSE, the protein name will be print out
unit	textual annotation for the dose unit, default is "min"
xtransform,	how should the xscale be transform, including the following ways: c("xsqrt","xcubert","xlog10","xlog2","xlinear"), corresponding to square-root, cube-root, log10, log2, and linear transformation
xinterval	a number indicating the numerical interval necessary for linear x-axis
layout	a vector indicating the panel layout for multi-panel plots per page, default value is c(5,5)
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 of the page
bottomlabel	textual label at the bottom of the page
leftlabel	textual label at the left side of the page
shadearea	a four element vector indicating the xmin, xmax, ymin, ymax for x and y axis for shading
shadeoutlinecolor	color used to shade the area, default value is black
shadefillcolor	color used to shade the area, default value is gray90
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_ITTR_ggplotting(ITTRdata_filtered[[1]], orderAUC=TRUE)

## End(Not run)

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