ms_IDIT_R2AUC: ms_IDIT_R2AUC

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

Description

Function to generate a R2 vs AUC plot for the ITDR or ITTR dataset The R2 (x-axis value), AUC (y-axis) and MDT/MTT (size of dot) are from the input data

Usage

ms_IDIT_R2AUC(
  data,
  nread = 10,
  printBothName = FALSE,
  printGeneName = TRUE,
  pfdatabase = FALSE,
  rep = "r",
  onlyshowstabilized = FALSE,
  simpleAUC = TRUE,
  preaveraged = FALSE,
  normalizedAUC = FALSE,
  refkeyword = "37C",
  AUC_uplimit = NULL,
  AUC_lowlimit = NULL,
  log2scale = FALSE,
  nMAD = 2.5,
  baselineMAD = 0,
  fcthreshold = 0,
  checkpointposition = NULL,
  keepreplicate = FALSE,
  keepfullrep = FALSE,
  stableref = FALSE,
  stableref_nMAD = 3.5,
  colorbackground = TRUE,
  graybackground = FALSE,
  nodesizebyMDT = TRUE,
  colornodes = TRUE,
  labelnodes = TRUE,
  yscale = NULL,
  PSMcutoff = TRUE,
  PSMthreshold = 3,
  PSMcutoffbycondition = FALSE,
  idtoshow = NULL,
  idtoexclude = NULL,
  plottitle = NULL,
  returnplot = FALSE
)

Arguments

data	ITDR or ITTR dataset to generate R2 vs AUC plot, the provided data should be associated with fitting parameters, i.e., after ms_ITDR_fitting or ms_ITTR_fitting
nread	number of reading channels or sample treatements, default value 10
printBothName	whether to print both gene name and protein name, default set to FALSE
printGeneName	whether to print only gene name, default set to TRUE, when both printBothName and printGeneName are FALSE, only the protein name is shown
pfdatabase	whether the data is a malaria dataset, default set to FALSE
rep	the rep indicator used in the naming of experimental conditions, such as "r", or "rep" or ""
onlyshowstabilized	whether to show only stablized hits, ie, direct targets, default set to FALSE
simpleAUC	whether to perform a simple calculation of AUC, default set to TRUE; note it is a bit "tricky" to interpret the AUC value in logarithmic space for most of ITDR data, suggest to just use simpleAUC by default
preaveraged	whether the data has already been averaged from replicates, default set to FALSE
normalizedAUC	whether to use the AUC values against a reference control such as 37C readings, default set to FALSE
refkeyword	a keyword used for the indication of reference control, as most of the time the reference is 37C expression level, default value is 37C
log2scale	whether to transform the readings into log2 scale, default set to FALSE
nMAD	level of significance of AUC values, default set at 2.5
baselineMAD	MAD of baseline variation, default value is 0
fcthreshold	short for fold change threshold, similar parameter as in ms_ITD/TR_filter() function, however this is an added-on selection feature in this R2AUC plot, and applied to the averaged (and/or normalized) data, so default value is 0
checkpointposition	referring to the positions of dose points to check whether their readings surpass fcthreshold, default value is NULL, which would automatically check the highest 3 dose points
keepreplicate	whether to only keep the curves that are measured with all replicates under at least one experimental conditions, default set to FALSE, when there is only one experimental condition in the dataset, this means only keep the full replicates, ie, same as keepfullrep=TRUE
keepfullrep	whether to only keep the curves that are measured with all replicates under all experimental conditions, default set to FALSE, this is useful for the dataset containing more than one experimental condition
stableref	whether to only keep the curves with stable/flat reference (most of the time, 37C) curves, default set to FALSE
stableref_nMAD	level of significance for control of the reference (most of the time, 37C) sample stability, default set at 3.5
colorbackground	whether to color the background with color and shape according to the condition, default set to TRUE
graybackground	whether to use gray color for the background but different shapes according to the condition, default set to FALSE
nodesizebyMDT	whether to set node size according to MDT/MTT value, ie the EC or ET column, default set to TRUE
colornodes	whether to fill the nodes in different colors if possible, default set to TRUE
labelnodes	whether to text-label the nodes, default set to TRUE
yscale	a two-element vector to indicate the y-axis scale for plotting if provided
PSMcutoff	whether to apply PSM threshold cutoff on hit selection, default set to TRUE
PSMthreshold	the minimal threshold of averaged PSM numbers to consider protein quantification as reliable, default value is 3
PSMcutoffbycondition	whether to apply PSM threshold cutoff on each experimental condition, otherwise on all the measured conditions, default set to FALSE
idtoshow	a vector containing the uniprot IDs to show on plot regardless they are hits or not
idtoexclude	a vector containing the uniprot IDs to exclude from plot
plottitle	a character used to label the title of the plot
returnplot	whether to retrieve the plot object, default set to FALSE

Examples

## Not run: 
ms_IDIT_R2AUC(ITDRdata_fitted)
ms_IDIT_R2AUC(ITDRdata_fitted, normalizedAUC=TRUE, stableref=TRUE, yscale=c(0.5,2))

## End(Not run)

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