NMF (version 0.2.2)

profplot: Plotting Expression Profiles

Description

Plotting Expression Profiles

When using NMF for clustering in particular, one looks for strong associations between the basis and a priori known groups of samples. Plotting the profiles may highlight such patterns.

Usage

profplot(x, ...)
  ## S3 method for class 'default':
profplot(x, y,
    scale = c("none", "max", "c1"), match.names = TRUE,
    legend = TRUE, confint = TRUE, Colv, labels,
    annotation, ..., add = FALSE)

Arguments

x

a matrix or an NMF object from which is extracted the mixture coefficient matrix. It is extracted from the best fit if x is the results from multiple NMF runs.

y

a matrix or an NMF object from which is extracted the mixture coefficient matrix. It is extracted from the best fit if y is the results from multiple NMF runs.

scale

specifies how the data should be scaled before plotting. If 'none' or NA, then no scaling is applied and the "raw" data is plotted. If TRUE or 'max' then each row of both matrices are normalised

match.names

a logical that indicates if the profiles in y should be subset and/or re-ordered to match the profile names in x (i.e. the rownames). This is attempted only when both x and y have names.

legend

a logical that specifies whether drawing the legend or not, or coordinates specifications passed to argument x of legend, that specifies the position of the legend.

confint

logical that indicates if confidence intervals for the R-squared should be shown in legend.

Colv

specifies the way the columns of x are ordered before plotting. It is used only when y is missing. It can be:

• a single numeric value, specifying the index of a row ofx, that is used to order the colu

labels

a character vector containing labels for each sample (i.e. each column of x). These are used for labelling the x-axis.

annotation

a factor annotating each sample (i.e. each column of x). If not missing, a coloured raw is plotted under the x-axis and annotates each sample accordingly. If argument Colv is a factor, then it is used to annotate the plot

...

graphical parameters passed to matplot or matpoints.

add

logical that indicates if the plot should be added as points to a previous plot

Details

The function can also be used to compare the profiles from two NMF models or mixture coefficient matrices. In this case, it draws a scatter plot of the paired profiles.

See Also

profcor

Examples

# roxygen generated flag
options(R_CHECK_RUNNING_EXAMPLES_=TRUE)

# create a random target matrix
v <- rmatrix(50, 10)

# fit a single NMF model
res <- nmf(v, 3)
profplot(res)

# ordering according to first profile
profplot(res, Colv=1) # increasing
profplot(res, Colv=-1) # decreasing

# fit a multi-run NMF model
res2 <- nmf(v, 3, nrun=3)
profplot(res2)

# draw a profile correlation plot: this show how the basis components are
# returned in an unpredictable order
profplot(res, res2)

# looking at all the correlations allow to order the components in a "common" order
profcor(res, res2)