Description Usage Arguments Value
Doing interactive CS analysis with PCA (Principal Component Analysis). This analysis is meant for 1 query signature.
Uses the PCA
function.
1 2 3 4 5 6 7 8 9 10 11 | ## S4 method for signature 'matrix,matrix,CSpca'
CSanalysis(querMat, refMat, type = "CSpca",
ncp = 5, scale.unit = TRUE, row.w = NULL, col.w = NULL, which = c(2,
3, 4, 5), component.plot = NULL, CSrank.queryplot = FALSE,
column.interest = NULL, row.interest = NULL, profile.type = "gene",
color.columns = NULL, gene.highlight = NULL, gene.thresP = 1,
gene.thresN = -1, thresP.col = "blue", thresN.col = "red",
grouploadings.labels = NULL, grouploadings.cutoff = NULL,
legend.names = NULL, legend.cols = NULL, legend.pos = "topright",
labels = TRUE, result.available = NULL, result.available.update = FALSE,
plot.type = "device", basefilename = NULL)
|
querMat |
Query matrix (Rows = genes and columns = compounds) |
refMat |
Reference matrix |
type |
|
ncp |
PCA Parameter: Number of dimensions kept in the results (by default 5). |
scale.unit |
PCA Parameter: A boolean, if TRUE (value set by default) then data are scaled to unit variance. |
row.w |
PCA Parameter: An optional row weights (by default, a vector of 1 for uniform row weights). |
col.w |
PCA Parameter: An optional column weights (by default, uniform column weights). |
which |
Choose one or more plots to draw:
|
component.plot |
Which components (Factor/Bicluster) should be investigated? Can be a vector of multiple (e.g. |
CSrank.queryplot |
Logical value deciding if the CS Rank Scores ( |
column.interest |
Numeric vector of indices of reference columns which should be in the profiles plots ( |
row.interest |
Numeric vector of gene indices to be plotted in gene profiles plot ( |
profile.type |
Type of
|
color.columns |
Vector of colors for the query and reference columns (compounds). If |
gene.highlight |
Single numeric vector or list of maximum 5 numeric vectors. This highlights gene of interest in gene scores plot ( |
gene.thresP |
Threshold for genes with a high score ( |
gene.thresN |
Threshold for genes with a low score ( |
thresP.col |
Color of genes above |
thresN.col |
Color of genes below |
grouploadings.labels |
This parameter used for the Group Loadings Plots (
Plot Please note that even when |
grouploadings.cutoff |
Parameter used in plot |
legend.names |
Option to draw a legend of for example colored columns in Compound Loadings plot ( |
legend.cols |
Colors to be used in legends. If |
legend.pos |
Position of the legend in all requested plots, can be |
labels |
Boolean value (default=TRUE) to use row and/or column text labels in the score plots ( |
result.available |
You can a previously returned object by |
result.available.update |
Logical value. If |
plot.type |
How should the plots be outputted? |
basefilename |
Directory including filename of the graphs if saved in pdf files |
An object of the S4 Class CSresult-class
.
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