rsgcc (version 1.0.6)

gcc.tsheatmap: correlaiton and clustering analysis of tissue-specific genes

Description

This function performs the correlaiton and clustering analysis of tissue-specific genes with expression data generated from microarray and RNA-Seq experiments.

Usage

gcc.tsheatmap(x,  cpus = 1,  ## correlation method method = c("GCC", "PCC", "SCC", "KCC", "BiWt", "MI", "MINE", "ED"),  distancemethod = c("Raw", "Abs", "Sqr"),  #cluster method clustermethod = c("complete", "average", "median",  "centroid", "mcquitty", "single", "ward"),  #hcdata by output gcc.tsheatmap  rowhcdata = NULL, colhcdata = NULL,       keynote = "FPKM",  ## dendrogram control symm = FALSE,  ## data scaling scale = c("none","row", "column"), na.rm=TRUE,
      ## image plot revC = identical(Colv, "Rowv"), add.expr,
      ## mapping data to colors breaks, symbreaks=min(x < 0, na.rm=TRUE) || scale!="none",
      ## colors colrange = c("yellow", "red"),   tissuecol= "heat.colors",
      ## block sepration colsep = 0.15, rowsep, sepcolor="white", sepwidth=c(0.05,0.05),  ## level trace trace=c("none","column","row","both"), tracecol="cyan", hline=median(breaks), vline=median(breaks), linecol=tracecol,
      ## plot margins margins = c(5, 5),
      ## plot labels main = NULL, xlab = NULL, ylab = NULL,
      ## plot layout lmat = NULL, lhei = NULL, lwid = NULL,
      ## extras ...)

Arguments

x

a data matrix containing numeric variables. Example: rows may correspond to genes and columns to samples.

cpus

the number of cpus used for correlaiton calcluation. snowfall package in R needed to be installed in advance.

method

a character string that specifies a correlation method to be used for association calculation.

distancemethod

a character string specifying the distance method to be used. Currently, three distance methods are available, include: "Raw" (1-cor)", "Abs" (1-|cor|), and "Sqr" (1-|cor|^2).

clustermethod

the distance measure to be used. This must be one of "complete", "average", "median", "centroid", "mcquitty", "single", or "ward".

rowhcdata

the object of class hc generated from gcc.hclust for rows in x.

colhcdata

the object of class hc generated from gcc.hclust for columns in x.

keynote

a character string indicating the lable of color key.

symm

logical indicating if x should be treated as a symmetrical matrix.

scale

a character string specifying if the data values would be centered and scaled by rows or by columns, or none.

na.rm

logical indicating whether the Nas should be eliminated.

revC

logical indicating if the column order should be reversed for plotting.

add.expr

expression that will be evaluated after the call to image.

breaks

(optional)Either a integer number specifying the break points to be used, or a numeric vector indicating the splitting points for binning x into colors.

symbreaks

Boolean indicating whether breaks should be made symmetric about 0. This option works if the quanbreaks is FALSE.

colrange

colors used for the image. It could be a function(i.e., heat.colors) or a vector of colors with at leat two elements (e.g., c("green", "black", "red")).

tissuecol

colors for tissues. tissuecol could be a function(i.e., heat.colors) or a vector of colors for different tissues.

colsep

(optional) vectors of integers indicating which columns should be seperated from the preceding columans by a narrow space of color sepcor.

rowsep

(optional) vectors of integers indicating which rows should be seperated from the preceding rows by a narrow space of color sepcor.

sepcolor

(optional) color used to seperate rows or columns.

sepwidth

(optional) A numeric vector containing two elements giving the width (colsep) or height (rowsep) for the seperation of columns or rows.

trace

character string indicating a solid "trace" lined should be drawn across "rows", or "column", or "both" or "none".

tracecol

color for trace

hline

vector of values whithin cells where horizontal lines should be drawn with line col.

vline

vector of values whithin cells where vertical lines should be drawn with line col.

linecol

color for hline and vline.

margins

a numeric vector containing 2 elements specifying the margins for column and row names, respectively. See (par(mar=*)).

main

main title. defaults to none.

xlab

x-axis label. defaults to none.

ylab

y-axis label. defaults to none.

lmat

position matrix for visual layout.

lhei

column height for visual layout.

lwid

column width for visual layout. For instance, lwid = c(0.5, 0.05, 0.01, 0.5, 0.01, 0.05, 0.5)

...

additonal arguments passed on to image.

Value

A list with the following components:

retval

a list with components of "rowInd" (row index of heat map from x), "colInd" (column index of heat map from x), "call" (the match call), "carpet" (reordered and scaled 'x' values used generate the main 'carpet'), "rowDendrogram" (row dendrogram), "colDendrogram" (column dendrogram), "breaks" (break points for binning x), "col" (colors used), and "colorTable" (a data frame providing the lower and upper bound and color for each bin).

hcr

the values returned from gcc.hclust function for clustering individuals (e.g., genes) in row direction

hcc

the values returned from gcc.hclust function for clustering individuals (e.g., genes) in column direction

See Also

gcc.dist, cor.matrix, gcc.hclust, gcc.tsheatmap.

Examples

## Not run: 
#    data(rsgcc)
#          
#    #get expression matrix of tissue-specific genes
#    tsRes <- getsgene(rnaseq, tsThreshold = 0.75, MeanOrMax = "Max", Fraction = TRUE)
# 
#    #heat map of tissue-specific genes
#    thm <- gcc.tsheatmap(tsRes$tsgene, cpus = 1, method = "GCC", 
#                     distancemethod = "Raw", clustermethod = "complete")
# ## End(Not run)