1. rcellminer
  2. man
  3. plotCellMiner.Rd
Browse code

Added importFrom statements Edited vignette to remove structure related sections Remove structure related tests Updated Rd files

cannin authored on 17/04/2020 15:48:36
Showing 1 changed files
man/plotCellMiner.Rd
History View file @ bbf5e46
... ... 
@@ -4,9 +4,19 @@
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 \alias{plotCellMiner}
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 \title{Description: Produces CellMiner-like plots in R}
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 \usage{
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-plotCellMiner(drugAct, molData, plots, nsc = NULL, gene = NULL,
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-  features = NULL, sub = NULL, xLimits = NULL, xLabel = NULL,
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-  extraPlot = NULL, verbose = FALSE)
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+plotCellMiner(
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+  drugAct,
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+  molData,
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+  plots,
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+  nsc = NULL,
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+  gene = NULL,
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+  features = NULL,
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+  sub = NULL,
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+  xLimits = NULL,
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+  xLabel = NULL,
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+  extraPlot = NULL,
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+  verbose = FALSE
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+)
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 }
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 \arguments{
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 \item{drugAct}{a matrix of drug activity values (cell lines as columns, drug entries as rows)}
... ... 
@@ -58,6 +68,4 @@ plotCellMiner(drugAct, molData, plots=NULL, nsc=NULL, features=c("mutCDK4",
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 \author{
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 Augustin Luna <augustin AT mail.nih.gov>
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 }
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-\concept{
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-rcellminer
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-}
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+\concept{rcellminer}
Browse code

Made changes for package testing and updated code for loading data packages

felloumi authored on 29/09/2017 19:53:15
Showing 1 changed files
man/plotCellMiner.Rd
History View file @ 4735142
... ... 
@@ -44,15 +44,15 @@ Description: Produces CellMiner-like plots in R
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 drugAct <- exprs(getAct(rcellminerData::drugData))
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 molData <- getMolDataMatrices()
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 plots <- c("mut", "drug", "cop", "xai", "pro")
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-plotCellMiner(drugAct, molData, plots=plots, nsc="94600", gene="CDK4", verbose=TRUE)
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+plotCellMiner(drugAct, molData, plots=plots, nsc="94600", gene="CDK4", verbose=FALSE)
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 plots <- c("mut", "xai", "cop", "cop", "cop", "cop")
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 plotCellMiner(drugAct, molData, plots=plots, nsc="94600", gene=c("CDK4", "TP53",
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-  "BRAF", "GAPDH"), verbose=TRUE)
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+  "BRAF", "GAPDH"), verbose=FALSE)
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-plotCellMiner(drugAct, molData, plots=plots, nsc=NULL, features=c("mutCDK4",
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-  "xaiCDK4", "exochr1:101704532_G_T", "mdais_p53_mut", "mirhsa-miR-22", "proTP53_26_GBL00064"),
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-  verbose=TRUE)
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+plotCellMiner(drugAct, molData, plots=NULL, nsc=NULL, features=c("mutCDK4",
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+  "xaiCDK4", "exochr1:101704532_G_T", "mdaIS_P53_MUT", "mirhsa-miR-22", "proTP53_26_GBL00064"),
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+  verbose=FALSE)
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 }
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 \author{
Browse code

Minor documentation update Updated analytics Updated about.md

cannin authored on 29/03/2017 21:43:19
Showing 1 changed files
man/plotCellMiner.Rd
History View file @ 15c7a76
... ... 
@@ -61,4 +61,3 @@ Augustin Luna <augustin AT mail.nih.gov>
61 61 
 \concept{
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 rcellminer
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 }
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-
Browse code

Adding parCorPatternComparison() function to do pattern comparisons based on partial correlations with respect to a fixed pattern (whose influence with respect to a linear model is to be excluded).

Vinodh N. Rajapakse authored on 09/08/2016 18:28:29
Showing 1 changed files
man/plotCellMiner.Rd
History View file @ 402a33e
... ... 
@@ -1,4 +1,4 @@
1 
-% Generated by roxygen2 (4.1.1): do not edit by hand
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+% Generated by roxygen2: do not edit by hand
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 % Please edit documentation in R/plotCellMiner.R
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 \name{plotCellMiner}
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 \alias{plotCellMiner}
... ... 
@@ -13,15 +13,15 @@ plotCellMiner(drugAct, molData, plots, nsc = NULL, gene = NULL,
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 \item{molData}{a list of matricies a molecular}
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-\item{plots}{a vector of characters denoting the plots to include and the order (e.g. c("mut", "drug", "cop").
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+\item{plots}{a vector of characters denoting the plots to include and the order (e.g. c("mut", "drug", "cop").
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 Currently, supported entries mutations (mut), drug activities (drug), copy number variations (cop)}
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 \item{nsc}{a string NSC ID that will be plotted when a "drug" entry appears in the plots vector}
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 \item{gene}{a string HUGO gene symbol for which the "mut", "cop", or "exp" plots will be produced if in plots vector}
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-\item{features}{a vector of strings that provide the full IDs for elements to be plotted (e.g. mutCDK4 for CDK4 mutations).
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-This overwrites the nsc and gene parameters, but is needed in advanced plots that involve data that involves one-to-many
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+\item{features}{a vector of strings that provide the full IDs for elements to be plotted (e.g. mutCDK4 for CDK4 mutations).
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+This overwrites the nsc and gene parameters, but is needed in advanced plots that involve data that involves one-to-many
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 relationships (e.g. many entries for a given gene in the exome data) and a gene symbol is ambiguous.}
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 \item{sub}{a vector of strings with sub-titles for each plot}
... ... 
@@ -47,12 +47,13 @@ plots <- c("mut", "drug", "cop", "xai", "pro")
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 plotCellMiner(drugAct, molData, plots=plots, nsc="94600", gene="CDK4", verbose=TRUE)
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 plots <- c("mut", "xai", "cop", "cop", "cop", "cop")
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-plotCellMiner(drugAct, molData, plots=plots, nsc="94600", gene=c("CDK4", "TP53",
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+plotCellMiner(drugAct, molData, plots=plots, nsc="94600", gene=c("CDK4", "TP53",
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   "BRAF", "GAPDH"), verbose=TRUE)
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-plotCellMiner(drugAct, molData, plots=plots, nsc=NULL, features=c("mutCDK4",
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-  "xaiCDK4", "exochr1:101704532_G_T", "mdais_p53_mut", "mirhsa-miR-22", "proTP53_26_GBL00064"),
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+plotCellMiner(drugAct, molData, plots=plots, nsc=NULL, features=c("mutCDK4",
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+  "xaiCDK4", "exochr1:101704532_G_T", "mdais_p53_mut", "mirhsa-miR-22", "proTP53_26_GBL00064"),
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   verbose=TRUE)
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+
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 }
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 \author{
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 Augustin Luna <augustin AT mail.nih.gov>
Browse code

Initial commit

cannin authored on 25/02/2016 02:26:31
Showing 1 changed files
man/plotCellMiner.Rd
History View file @ 7ec0960
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new file mode 100644
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@@ -0,0 +1,63 @@
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+% Generated by roxygen2 (4.1.1): do not edit by hand
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+% Please edit documentation in R/plotCellMiner.R
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+\name{plotCellMiner}
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+\alias{plotCellMiner}
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+\title{Description: Produces CellMiner-like plots in R}
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+\usage{
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+plotCellMiner(drugAct, molData, plots, nsc = NULL, gene = NULL,
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+  features = NULL, sub = NULL, xLimits = NULL, xLabel = NULL,
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+  extraPlot = NULL, verbose = FALSE)
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+}
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+\arguments{
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+\item{drugAct}{a matrix of drug activity values (cell lines as columns, drug entries as rows)}
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+
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+\item{molData}{a list of matricies a molecular}
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+
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+\item{plots}{a vector of characters denoting the plots to include and the order (e.g. c("mut", "drug", "cop").
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+Currently, supported entries mutations (mut), drug activities (drug), copy number variations (cop)}
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+
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+\item{nsc}{a string NSC ID that will be plotted when a "drug" entry appears in the plots vector}
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+
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+\item{gene}{a string HUGO gene symbol for which the "mut", "cop", or "exp" plots will be produced if in plots vector}
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+
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+\item{features}{a vector of strings that provide the full IDs for elements to be plotted (e.g. mutCDK4 for CDK4 mutations).
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+This overwrites the nsc and gene parameters, but is needed in advanced plots that involve data that involves one-to-many
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+relationships (e.g. many entries for a given gene in the exome data) and a gene symbol is ambiguous.}
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+
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+\item{sub}{a vector of strings with sub-titles for each plot}
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+
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+\item{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)}
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+
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+\item{xLabel}{a string for the default X-axis label}
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+
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+\item{extraPlot}{a list containing title, label, and values (numeric vector of length 60); only one extra plot can be included}
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+
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+\item{verbose}{a boolean to show debugging information}
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+}
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+\value{
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+None
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+}
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+\description{
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+Description: Produces CellMiner-like plots in R
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+}
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+\examples{
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+drugAct <- exprs(getAct(rcellminerData::drugData))
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+molData <- getMolDataMatrices()
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+plots <- c("mut", "drug", "cop", "xai", "pro")
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+plotCellMiner(drugAct, molData, plots=plots, nsc="94600", gene="CDK4", verbose=TRUE)
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+
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+plots <- c("mut", "xai", "cop", "cop", "cop", "cop")
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+plotCellMiner(drugAct, molData, plots=plots, nsc="94600", gene=c("CDK4", "TP53",
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+  "BRAF", "GAPDH"), verbose=TRUE)
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+
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+plotCellMiner(drugAct, molData, plots=plots, nsc=NULL, features=c("mutCDK4",
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+  "xaiCDK4", "exochr1:101704532_G_T", "mdais_p53_mut", "mirhsa-miR-22", "proTP53_26_GBL00064"),
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+  verbose=TRUE)
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+}
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+\author{
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+Augustin Luna <augustin AT mail.nih.gov>
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+}
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+\concept{
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+rcellminer
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+}
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+