KRIS (version 1.1.1)

plot3views: Create scatter plots in three views.

Description

Visualize data in X-Y plane, X-Z plane, and Y-Z plane. The input object (matrix or data.frame) must contain at least 3 columns.

Usage

plot3views(X, labels, col.pat.table = NA, only.row = NA)

Arguments

X

A matrix or a data.frame that contains at least 3 columns of numeric data. If there are more than 3 columns in X, only the first 3 columns will be used.

labels

A vector containing row labels of X for display. All vector elements should be of type "character" (as.character). The length of vector equals the number of rows in X.

col.pat.table

A data.frame that associates colors and patterns to row labels (see labels before). It needs to contain 3 columns which represent unique labels (column 1) and associated patterns (column 2) and colors (column 3). Default = NA.

only.row

A vector that contains subset of row numbers that are selected to be plotted. Default = NA.

Details

col.pat.table needs to be set properly. For example, given the vector labels consists of 5 elements as in c('pop1','pop2','pop2','pop2', 'pop1'), the data.frame col.pat.table must contain 2 rows corresponding to 'pop1' and 'pop2', and 3 columns to describe their characteristics (i.e. patterns and colors). See the section "Examples" for more details.

Examples

# NOT RUN {
#Load simulated dataset
data(example_SNP)

PCs <- cal.pc.linear(simsnp$snp, no.pc = 3)
plot3views( PCs$PC, sample_labels)

#To change colors and patterns using symbols
all.labels <- unique(sample_labels)
my.colors <- c('pink', 'yellow', 'cyan', 'green')
my.patterns<- c(0,1,2,3)
my.table <- data.frame(all.labels, my.patterns, my.colors)
plot3views(PCs$PC, labels = sample_labels, col.pat.table = my.table)

#To change colors and patterns using characters
my.patterns<- c('o', 'x', '&', '#')
#Use cbind to keep my.patterns as 'character'
my.table <- cbind(all.labels, my.patterns, my.colors)
plot3views(PCs$PC, labels = sample_labels, col.pat.table = my.table)
# }