Matrix plotting {OceanView}

Functions for plotting matrices, or for splitting them and for maing suitable summaries

Description

Mplot plots data from (a list of) matrices.

Msplit splits a matrix in a list according to factors (or unique values).

Mcommon creates a list of matrices that have only common variables.

Msummary and Mdescribe create suitable summaries of all columns of a matrix or list.

Usage

  Mplot (M, ..., x = 1, select = NULL, which = select, 
         subset = NULL, ask = NULL, 
         legend = list(x = "center"), pos.legend = NULL,
         xyswap = FALSE, rev = "") 

  Msummary (M, ..., 
         select = NULL, which = select, 
         subset = NULL) 

  Mdescribe (M, ..., 
         select = NULL, which = select, 
         subset = NULL) 

  Msplit (M, split = 1, subset = NULL) 

  Mcommon (M, ..., verbose = FALSE)      

Arguments

M

Matrix or data.frame to be plotted, or treated. For Mplot, M can be a list with matrices or data.frames.

x

Name or number of the column to be used as the x-values.

select

Which variable/columns to be selected. This is added for consistency with the R-function subset.

which

The name(s) or the index to the variables that should be plotted or selected. Default = all variables, except time.

subset

Logical expression indicating elements or rows to keep in select: missing values are taken as FALSE

ask

Logical; if TRUE, the user is asked before each plot, if NULL the user is only asked if more than one page of plots is necessary and the current graphics device is set interactive, see par(ask) and dev.interactive.

legend

A list with parameters for the legend to be added. If FALSE, then no legend will be drawn.

pos.legend

The position of the legend, a number. The default is to put the legend in the last figure. Also allowed is pos.legend = 0, which will create a new figure with only the legend.

xyswap

If TRUE, then the x- and y-values will be swapped.

rev

a character string which contains "x" if the x axis is to be reversed, "y" if the y axis is to be reversed and "xy" or "yx" if both axes are to be reversed.

split

The name or number of the column with the factor according to which the matrix will be split.

verbose

If TRUE will write output to the screen.

...

Additional arguments passed to the methods. For Mplot: can also be extra matrices to plot. The arguments after ... must be matched exactly.

Value

Function Msplit returns a list with the matrices, split according to the factors; the names of the elements is set by the factor's name. It is similar to the R-function split.

Function Mcommon returns a list with the matrices, which only have the common variables.

Function Msummary returns a data.frame with summary values (minimum, first quantile, median, mean, 3rd quantile, maximum) for each column of the input (variable). If there are more than one object to be summarised, or if M is a list of objects, the name of the object is in the second column.

Function Mdescribe returns a data.frame with summary values (number of data, number of missing values, number of unique values, mean value, the standard deviation, the minimum, the p = 0.05, 0.1, 0.5, 0.9, 0.95 quantiles, and the maximum) for each column of the input (variable). If there are more than one object to be summarised, or if M is a list of objects, the name of the object is in the second column.

Author(s)

Karline Soetaert <[e-mail]>

Examples

# save plotting parameters
 pm <- par("mfrow")

## =======================================================================
## Create three dummy matrices
## =======================================================================

 M1 <- matrix(nrow = 10, ncol = 5, data = 1:50)
 colnames(M1) <- LETTERS[1:5]

 M2 <- M1[, c(1, 3, 4, 5, 2)] 
 M2[ ,-1] <- M2[,-1] /2
 colnames(M2)[3] <- "CC"  # Different name

 M3 <- matrix(nrow = 5, ncol = 4, data = runif(20)*10) 
 M3[,1] <- sort(M3[,1])
 colnames(M3) <- colnames(M1)[-3]

# show them
 head(M1); head(M2); head(M3)
 Msummary(M1)
 Msummary(M1, M2, M3)

# plot all columns of M3 -  will change mfrow 
 Mplot(M3, type = "b", pch = 18, col = "red")

# plot results of all three data sets
 Mplot(M1, M2, M3, lwd = 2, mtext = "All variables versus 1st column",
       legend = list(x = "top", legend = c("M1", "M2", "M3")))


## =======================================================================
## Plot a selection or only common elements
## =======================================================================

 Mplot(M1, M2, M3, x = "B", select = c("A", "E"), pch = c(NA, 16, 1), 
       type = c("l", "p", "b"), col = c("black", "red", "blue"),  
       legend = list(x = "right", legend = c("M1", "M2", "M3")))

 Mplot(Mcommon(M1, M2, M3), lwd = 2, mtext = "common variables", 
       legend = list(x = "top", legend = c("M1", "M2", "M3")))

 Mdescribe(Mcommon(M1, M2, M3))
 
## =======================================================================
## The iris and Orange data set
## =======================================================================

# Split the matrix according to the species
 Irislist <- Msplit(iris, split = "Species")
 names(Irislist)
 
 Mdescribe(Irislist, which = "Sepal.Length")
 Mdescribe(iris, which = "Sepal.Length", subset = Species == "setosa")

# legend in a separate plot
 Mplot(Irislist, type = "p", pos.legend = 0,
       legend = list(x = "center", title = "species"))

 Mplot(Msplit(Orange,1), lwd = 2,
       legend = list(x = "topleft", title = "tree nr"))
 Msummary(Msplit(Orange,1))

# reset plotting parameters
 par(mfrow = pm)