Description Usage Arguments Details Value Examples
View source: R/pophelperSpatial.R
Plot runs spatially and colour individuals by max assignment cluster.
1 2 3 4 5 6 7 8 9 10 | 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 |
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 |
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 |
width |
A numeric indicating the the width of export figure. Default in cm unless units are changed. If |
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 |
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ## 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)
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