visDmatCluster {supraHex} | R Documentation

## Function to visualise clusters/bases partitioned from a supra-hexagonal grid

### Description

`visDmatCluster` is supposed to visualise clusters/bases partitioned from a supra-hexagonal grid

### Usage

    visDmatCluster(
    sMap,
    sBase,
    height = 7,
    margin = rep(0.1, 4),
    area.size = 1,
    gp = grid::gpar(cex = 0.8, font = 2, col = "black"),
    border.color = "transparent",
    fill.color = NULL,
    lty = 1,
    lwd = 1,
    lineend = "round",
    linejoin = "round",
    colormap = c("rainbow", "jet", "bwr", "gbr", "wyr", "br", "yr", "wb"),
    clip = c("on", "inherit", "off"),
    newpage = TRUE
    )

### Arguments

`sMap` | an object of class "sMap"
`sBase` | an object of class "sBase"
`height` | a numeric value specifying the height of device
`margin` | margins as units of length 4 or 1
`area.size` | an inteter or a vector specifying the area size of each hexagon
`gp` | an object of class "gpar". It is the output from a call to the function "gpar" (i.e., a list of graphical parameter settings)
`border.color` | the border color for each hexagon
`fill.color` | the filled color for each hexagon
`lty` | the line type for each hexagon. 0 for 'blank', 1 for 'solid', 2 for 'dashed', 3 for 'dotted', 4 for 'dotdash', 5 for 'longdash', 6 for 'twodash'
`lwd` | the line width for each hexagon
`lineend` | the line end style for each hexagon. It can be one of 'round', 'butt' and 'square'
`linejoin` | the line join style for each hexagon. It can be one of 'round', 'mitre' and 'bevel'
`colormap` | short name for the colormap. It can be one of "jet" (jet colormap), "bwr" (blue-white-red colormap), "gbr" (green-black-red colormap), "wyr" (white-yellow-red colormap), "br" (black-red colormap), "yr" (yellow-red colormap), "wb" (white-black colormap), and "rainbow" (rainbow colormap, that is, red-yellow-green-cyan-blue-magenta). Alternatively, any hyphen-separated HTML color names, e.g. "blue-black-yellow", "royalblue-white-sandybrown", "darkgreen-white-darkviolet". A list of standard color names can be found in http://html-color-codes.info/color-names
`clip` | either "on" for clipping to the extent of this viewport, "inherit" for inheriting the clipping region from the parent viewport, or "off" to turn clipping off altogether
`newpage` | logical to indicate whether to open a new page. By default, it sets to true for opening a new page

### Value

invisible

### Note

none

### See Also

`sDmatCluster`, `sDmat`, `visColormap`, `visHexGrid`

### Examples

    # 1) generate an iid normal random matrix of 100x10
    data <- matrix( rnorm(100*10,mean=0,sd=1), nrow=100, ncol=10)

    ## Not run:
    # 2) get trained using by default setup
    sMap <- sPipeline(data=data)

    # 3) partition the grid map into clusters using region-growing algorithm
    sBase <- sDmatCluster(sMap=sMap, which_neigh=1,
    distMeasure="median", clusterLinkage="average")

    # 4) visualise clusters/bases partitioned from the sMap
    visDmatCluster(sMap,sBase)
    # 4a) also, the area size is proportional to the hits
    visDmatCluster(sMap,sBase, area.size=log2(sMap$hits+1))
    # 4b) also, the area size is inversely proportional to the map distance
    dMat <- sDmat(sMap)
    visDmatCluster(sMap,sBase, area.size=-1*log2(dMat))

    # 5) customise the fill color and line type
    my_color <-
    visColormap(colormap="PapayaWhip-pink-Tomato")(length(sBase$seeds))[sBase$bases]
    my_lty <- (sBase$bases %% 2)
    visDmatCluster(sMap,sBase, fill.color=my_color, lty=my_lty,
    border.color="black", lwd=2, area.size=0.9)
    # also, the area size is inversely proportional to the map distance
    visDmatCluster(sMap,sBase, fill.color=my_color, lty=my_lty,
    border.color="black", lwd=2, area.size=-1*log2(dMat))

    ## End(Not run)

[Package supraHex version 1.28.2 Index]