qlists

Description Usage Arguments Details Value Examples

View source: R/pophelperSpatial.R

Plot runs spatially and colour individuals by max assignment cluster.

plotQSpatial(qlist = NULL, coords = NULL, clustercol = NA,
  setutm = FALSE, imgtype = "png", height = NA, width = NA,
  units = "cm", res = 200, showaxis = FALSE, coordsratio = NA,
  plotcolour = "grey30", pointcol = "grey10", pointtype = "+",
  pointsize = 4, pointalpha = 0.9, chull = FALSE, chullalpha = 0.02,
  chullsize = 0.4, chulltype = 1, ellipse = TRUE, ellconf = 0.95,
  ellsize = 0.4, elltype = 1, ellpoints = 100, legend = TRUE,
  legendlab = NA, legendpos = c(0.99, 0.99), legendjust = c(1, 1),
  legendkeysize = NA, legendtextsize = NA, plottitle = NULL,
  exportplot = TRUE, exportfilename = NA, dataout = FALSE)

`qlist`	A qlist (list of dataframes) with one element. An output from `readQ` with one element.
`coords`	A dataframe. The number of rows must be equal to the number of samples in qlist. The dataframe must have 2 columns in the order: x (latitude) and then y (longitude). Coordinates must be in standard longitude latitude (LL) decimals.
`clustercol`	A vector of colours for the clusters. R colour names or hexadecimal values. If NA, colours are automatically generated. K 1 to 12 are custom unique colours while K>12 are coloured by function `rich.color()`.
`setutm`	A logical. If TRUE, then LL coordinates are converted to UTM coordinates. The midpoint of the longitude within the dataset is used to determine the UTM zone.
`imgtype`	A character indicating the export format for figures. Options are "png", "jpeg" or "pdf". If pdf, height and width must be in inches and res argument is ignored (set to 300).
`height`	A numeric indicating the height of export figure. Default in cm unless units are changed. If `imgtype` is pdf, then height must be in inches.
`width`	A numeric indicating the the width of export figure. Default in cm unless units are changed. If `imgtype` is pdf, then height must be in inches.
`units`	A character indicating the units of measurement for figure dimensions. "cm", "mm" or "in".
`res`	A numeric indicating the pixel resolution of the export image. Set to 200 by default.
`showaxis`	A logical indicating if the axis text, axis ticks and plot border are plotted.
`coordsratio`	A numeric indicating ratio between x and y axes. If set to 1, then 1 unit on x axis is the same as 1 unit on y axis.
`plotcolour`	A character R colour or hexadecimal denoting colour for plot elements. Defaults to "grey30".
`pointcol`	The colour character for sample points. An R colour or hexadecimal value.
`pointtype`	The shape/pch of sample points. A numeric or a character. By default, "+" is used for all points. If NA, then each cluster is plotted using a different shape. If a numeric or character of length one is used, then it is used for all points. If a vector is used, then it must be equal to number clusters.
`pointsize`	A numeric indicating the size of sample points. A number usually 0.4,0.8,1,3 etc.
`pointalpha`	A numeric between 0 and 1 indicating the transparency of points.
`chull`	A logical indicating if the convex hull is computed for each cluster. The outer points of each cluster are connected by lines. If less than 3 points are available in a cluster, then convex hull is not computed and a warning is shown.
`chullalpha`	A numeric between 0 and 1 indicating the transparency of the convex hull.
`chullsize`	A numeric indicating the thickness of the convex hull border.
`chulltype`	A numeric indicating the line type of the convex hull border. Option pch in standard R.
`ellipse`	A logical indicating if an ellipse around the clusters. Set to F to supress ellipse.
`ellconf`	A numeric indicating the confidence interval of the ellipse. Defaults to 0.95.
`ellsize`	A numeric indicating the thickness of the ellipse line.
`elltype`	A numeric indicating the linetype for the ellipse. Option lty in standard R.
`ellpoints`	A numeric indicating the number of points on the ellipse.
`legend`	A logical indicating if the legend for the colours is plotted.
`legendlab`	A vector of labels for the legend denoting clusters. Defaults to cluster numbers.
`legendpos`	A character or 2-value numeric vector indicating the position of the legend. If "right","left","top" or "bottom", then, legend is plotted outside the plot area. To plot inside plot area use a 2 vale vector. If a vector like c(1,1), first value denotes x-axis from 0 to 1 and second value denotes y-axis from 0 to 1. For ex. to plot in bottom left corner, use c(0,0).
`legendjust`	The x and y axis justification of the legend. A 2-value vector.
`legendkeysize`	A numeric indicating the size of the legend in cm. Usually values like 0.5,0.7,1.2 etc.
`legendtextsize`	A numeric indicating the size of the text in the legend.
`plottitle`	A character for the title of the plot. NULL by default.
`exportplot`	If set to FALSE, no image is exported.
`exportfilename`	A character name for the export figure. Automatically computed if NA.
`dataout`	A logical. If set to TRUE, a list of one or more `ggplot` gtable elements are returned. This output can be modified using `ggplot` themes() for more figure control if required.

The coordinates must always be provided as standard longitude-latitude (LL) decimal format.

If dataout=T, a list of one or more ggplot gtable output is returned for more theme control if required.

## Not run: 
#structure file
q <- readQ(system.file("files/Structure239_4",package="pophelperSpatial"))
xy <- read.delim(system.file("files/coords239.txt",package="pophelperSpatial"),header=F)

# basic usage
plotQSpatial(qlist=q,coords=xy)
# set UTM coordinates. Better geographic distance representation over a scale such as countries.
plotQSpatial(q,xy,height=12,setutm=T)
# without ellipses
plotQSpatial(q,xy,height=12,ellipse=F)
# show axis
plotQSpatial(q,xy,height=12,showaxis=T)
# change plot element colours
plotQSpatial(q,xy,height=12,showaxis=T,plotcolour="blue")

## End(Not run)