Description Usage Arguments Value
Doing interactive CS analysis with FABIA (Factor Analysis for Bicluster Acquisition). One or multiple query compounds are possible in this analysis.
1 2 3 4 5 6 7 8 9 10 11 12 13 | ## S4 method for signature 'matrix,matrix,CSfabia'
CSanalysis(querMat, refMat,
type = "CSfabia", p = 13, alpha = 0.01, cyc = 500, spl = 0,
spz = 0.5, non_negative = 0, random = 1, center = 2, norm = 1,
scale = 0, lap = 1, nL = 0, lL = 0, bL = 0, 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 |
|
p |
Fabia Parameter: number of hidden factors = number of biclusters; default = 13 |
alpha |
Fabia Parameter: sparseness loadings (0 - 1.0); default = 0.01 |
cyc |
Fabia Parameter: number of iterations; default = 500 |
spl |
Fabia Parameter: sparseness prior loadings (0 - 2.0); default = 0 (Laplace) |
spz |
Fabia Parameter: sparseness factors (0.5 - 2.0); default = 0.5 (Laplace) |
non_negative |
Fabia Parameter: Non-negative factors and loadings if non_negative > 0; default = 0 |
random |
Fabia Parameter: <=0: by SVD, >0: random initialization of loadings in [-random,random]; default = 1.0 |
center |
Fabia Parameter: data centering: 1 (mean), 2 (median), > 2 (mode), 0 (no); default = 2 |
norm |
Fabia Parameter: data normalization: 1 (0.75-0.25 quantile), >1 (var=1), 0 (no); default = 1 |
scale |
Fabia Parameter: loading vectors are scaled in each iteration to the given variance. 0.0 indicates non scaling; default = 0.0 |
lap |
Fabia Parameter: minimal value of the variational parameter; default = 1.0 |
nL |
Fabia Parameter: maximal number of biclusters at which a row element can participate; default = 0 (no limit) |
lL |
Fabia Parameter: maximal number of row elements per bicluster; default = 0 (no limit) |
bL |
Fabia Parameter: cycle at which the nL or lL maximum starts; default = 0 (start at the beginning) |
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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