Newly tracked file
R/visualize_phyloregions.R
changed.
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man/plot.phyloregion.Rd
has changed.
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@@ -35,6 +35,7 @@
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| 35 | 35 | #' scaling color space matching the color vision of the human visual |
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| 36 | 36 | #' system. The name is matched to the list of available color palettes from |
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| 37 | 37 | #' the \code{hcl.colors} function in the \code{grDevices} package. |
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| 38 | + | #' @param col vector of colors of length equal to the number of phyloregions. |
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| 38 | 39 | #' @param shp a polygon shapefile of grid cells. |
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| 39 | 40 | #' @param \dots arguments passed among methods. |
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| 40 | 41 | #' @return No return value, called for plotting. |
@@ -45,15 +46,22 @@
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| 45 | 46 | #' @importFrom graphics plot plot.default |
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| 46 | 47 | #' @rawNamespace export(plot.phyloregion) |
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| 47 | 48 | #' @export |
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| 48 | - | plot.phyloregion <- function(x, shp=NULL, palette="NMDS", ...) { |
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| 49 | + | plot.phyloregion <- function(x, shp=NULL, palette="NMDS", col=NULL, ...) { |
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| 49 | 50 | if (!inherits(x, "phyloregion")) |
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| 50 | 51 | stop("object \"x\" is not of class \"phyloregion\"") |
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| 51 | 52 | if(is.null(shp)) shp <- x$shp |
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| 52 | 53 | if(is.null(shp)) stop("Need shape file!") |
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| 53 | 54 | k <- x$k |
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| 54 | - | if(palette=="NMDS") clr <- shp$COLOURS |
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| 55 | - | else clr <- hcl.colors(k, palette)[shp$cluster] |
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| 56 | - | plot(shp, col = clr, ...) |
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| 55 | + | #l <- length(shp$cluster) |
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| 56 | + | if(is.null(col)){ |
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| 57 | + | if(palette=="NMDS") col <- shp$COLOURS |
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| 58 | + | else col <- hcl.colors(k, palette)[shp$cluster] |
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| 59 | + | } |
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| 60 | + | else{ |
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| 61 | + | if(length(col)==k) col <- col[shp$cluster] |
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| 62 | + | else stop("Expect 'col' of length x$k!") |
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| 63 | + | } |
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| 64 | + | plot(shp, col = col, ...) |
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| 57 | 65 | text(shp, labels = as.character(shp@data$cluster), ...) |
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| 58 | 66 | } |
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| 59 | 67 |
| Files | Coverage |
|---|---|
| R | 7.87% |
| Project Totals (37 files) | 7.87% |
275.1
275.2
Sunburst
The inner-most circle is the entire project, moving away from the center are folders then, finally, a single file.
The size and color of each slice is representing the number of statements and the coverage, respectively.
Icicle
The top section represents the entire project. Proceeding with folders and finally individual files.
The size and color of each slice is representing the number of statements and the coverage, respectively.
