Mercurial > repos > ecology > obisindicators

annotate visualize.r @ 4:8ca01a4cfd27 draft default tip

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 13ac67c0a21d742b29e6273cdff058560abad770
author ecology
date Tue, 05 Nov 2024 14:17:36 +0000
parents 7899febbfb94
children
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7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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1 #' Statically map indicators using ggplot
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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2 #'
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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3 #' @param grid spatial features, e.g. hexagons, to plot; requires a geometry
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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4 #' spatial column
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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5 #' @param column column name with indicator; default="shannon"
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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6 #' @param label label to show on legend
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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7 #' @param crs coordinate reference system; see `sf::st_crs()`
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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8 #' @param trans For continuous scales, the name of a transformation object or
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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9 #' the object itself. Built-in transformations include "asn", "atanh",
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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10 #' "boxcox", "date", "exp", "hms", "identity" (default), "log", "log10", "log1p",
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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11 #' "log2", "logit", "modulus", "probability", "probit", "pseudo_log",
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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12 #' "reciprocal", "reverse", "sqrt" and "time". See `ggplot2::continuous_scale`
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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13 #'
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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14 #' @return ggplot2 plot
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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15 #' @concept visualize
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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16 #' @export
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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17 #' @import rnaturalearth viridis ggplot2
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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18 #'
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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19 #' @examples
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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20 gmap_indicator <- function(
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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21 grid, column = "shannon", label = "Shannon index", trans = "identity",
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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22 crs = "+proj=robin +lon_0=0 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84 +units=m +no_defs") {
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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23
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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24 world <- rnaturalearth::ne_countries(scale = "medium", returnclass = "sf")
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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25 bb <- sf::st_bbox(
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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26 sf::st_transform(grid, crs))
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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28 ggplot2::ggplot() +
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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29 ggplot2::geom_sf(
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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30 data = grid, ggplot2::aes_string(
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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31 fill = column, geometry = "geometry"), lwd = 0) +
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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32 viridis::scale_color_viridis(
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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33 option = "inferno", na.value = "white",
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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34 name = label, trans = trans) +
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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35 viridis::scale_fill_viridis(
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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36 option = "inferno", na.value = "white",
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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37 name = label, trans = trans) +
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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38 ggplot2::geom_sf(
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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39 data = world, fill = "#dddddd", color = NA) +
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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40 ggplot2::theme(
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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41 panel.grid.major.x = ggplot2::element_blank(),
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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42 panel.grid.major.y = ggplot2::element_blank(),
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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43 panel.grid.minor.x = ggplot2::element_blank(),
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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44 panel.grid.minor.y = ggplot2::element_blank(),
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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45 panel.background = ggplot2::element_blank(),
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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46 axis.text.x = ggplot2::element_blank(),
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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47 axis.text.y = ggplot2::element_blank(),
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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48 axis.ticks = ggplot2::element_blank(),
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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49 axis.title.x = ggplot2::element_blank(),
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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50 axis.title.y = ggplot2::element_blank()) +
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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51 ggplot2::xlab("") + ggplot2::ylab("") +
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52 ggplot2::coord_sf(
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53 crs = crs,
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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54 xlim = bb[c("xmin", "xmax")],
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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55 ylim = bb[c("ymin", "ymax")])
7899febbfb94 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators commit 1e0b3b101d2380338030e607e6949331439c6dfc
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56 }