Description Usage Arguments Value
Doing interactive CS analysis with MFA (Multiple Factor Analysis). Should use multiple references for this analysis.
1 2 3 4 5 6 7 8 9 10 11 | ## S4 method for signature 'matrix,matrix,CSmfa'
CSanalysis(refMat, querMat, type = "CSmfa",
ncp = 5, weight.col.mfa = NULL, row.w = NULL, which = c(2, 3, 4, 5),
component.plot = NULL, CSrank.refplot = 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", result.available = NULL,
result.available.update = FALSE, plot.type = "device",
basefilename = "analyseMFA")
|
refMat |
Reference matrix (Rows = genes and columns = compounds) |
querMat |
Query matrix |
type |
|
ncp |
MFA Parameter: Number of dimensions kept in the results (by default 5). |
weight.col.mfa |
MFA Parameter: Vector of weights, useful for HMFA method (by default, |
row.w |
MFA Parameter: An optional row weights (by default, a vector of 1 for uniform row 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.refplot |
Logical value deciding if the CS Rank Scores ( |
column.interest |
Numeric vector of indices of query 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 reference and query 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 |
result.available |
You can a previously returned object by |
result.available.update |
Logical value. If |
plot.type |
How should the plots be outputted? |
basefilename |
Basename of the graphs if saved in pdf files |
An object of the S4 Class CSresult
.
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