plotCellMiner: Description: Produces CellMiner-like plots in R

In rcellminer: rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines

Description

Description: Produces CellMiner-like plots in R

Usage

plotCellMiner(
  drugAct,
  molData,
  plots,
  nsc = NULL,
  gene = NULL,
  features = NULL,
  sub = NULL,
  xLimits = NULL,
  xLabel = NULL,
  extraPlot = NULL,
  verbose = FALSE
)

Arguments

drugAct	a matrix of drug activity values (cell lines as columns, drug entries as rows)
molData	a list of matricies a molecular
plots	a vector of characters denoting the plots to include and the order (e.g. c("mut", "drug", "cop"). Currently, supported entries mutations (mut), drug activities (drug), copy number variations (cop)
nsc	a string NSC ID that will be plotted when a "drug" entry appears in the plots vector
gene	a string HUGO gene symbol for which the "mut", "cop", or "exp" plots will be produced if in plots vector
features	a vector of strings that provide the full IDs for elements to be plotted (e.g. mutCDK4 for CDK4 mutations). This overwrites the nsc and gene parameters, but is needed in advanced plots that involve data that involves one-to-many relationships (e.g. many entries for a given gene in the exome data) and a gene symbol is ambiguous.
sub	a vector of strings with sub-titles for each plot
xLimits	a 2 number vector with the the minimum and maximum X-axis values (default: -3,3 for Z-scores, 0,1 for binary entries)
xLabel	a string for the default X-axis label
extraPlot	a list containing title, label, and values (numeric vector of length 60); only one extra plot can be included
verbose	a boolean to show debugging information

Value

None

Author(s)

Augustin Luna <augustin AT mail.nih.gov>

Examples

drugAct <- exprs(getAct(rcellminerData::drugData))
molData <- getMolDataMatrices()
plots <- c("mut", "drug", "cop", "xai", "pro")
plotCellMiner(drugAct, molData, plots=plots, nsc="94600", gene="CDK4", verbose=FALSE)

plots <- c("mut", "xai", "cop", "cop", "cop", "cop")
plotCellMiner(drugAct, molData, plots=plots, nsc="94600", gene=c("CDK4", "TP53", 
  "BRAF", "GAPDH"), verbose=FALSE)

plotCellMiner(drugAct, molData, plots=NULL, nsc=NULL, features=c("mutCDK4", 
  "xaiCDK4", "exochr1:101704532_G_T", "mdaIS_P53_MUT", "mirhsa-miR-22", "proTP53_26_GBL00064"), 
  verbose=FALSE)

rcellminer documentation built on Nov. 26, 2020, 2:02 a.m.