NMF (version 0.16.1)

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 = FALSE,
    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

a logical that specifies whether the columns of the matrices should be scaled into proportions (i.e. to sum up to one) before plotting. Default is FALSE.

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

# 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)