diff --git a/doc/.ipynb_checkpoints/Color gradient examples-checkpoint.ipynb b/doc/.ipynb_checkpoints/Color gradient examples-checkpoint.ipynb new file mode 100644 index 0000000..8ef8789 --- /dev/null +++ b/doc/.ipynb_checkpoints/Color gradient examples-checkpoint.ipynb @@ -0,0 +1,485 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Example plots to show color themes included in SpatialEcology.jl\n", + "To use the themes when plotting with Plots.jl, simply call `registercolors()`, and the gradients become available " + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Loading data\n", + "For this example we use the global species richness pattern of amphibians, based on data from IUCN." + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": { + "collapsed": false + }, + "outputs": [ + { + "data": { + "text/html": [ + "
LongLatWorldMapID_Bufo_arabicus
1-72.5-54.5519480
2-71.5-54.5519490
3-70.5-54.5519500
4-74.5-53.5515860
" + ], + "text/plain": [ + "4×4 DataFrames.DataFrame\n", + "│ Row │ Long │ Lat │ WorldMapID │ _Bufo_arabicus │\n", + "├─────┼───────┼───────┼────────────┼────────────────┤\n", + "│ 1 │ -72.5 │ -54.5 │ 51948 │ 0 │\n", + "│ 2 │ -71.5 │ -54.5 │ 51949 │ 0 │\n", + "│ 3 │ -70.5 │ -54.5 │ 51950 │ 0 │\n", + "│ 4 │ -74.5 │ -53.5 │ 51586 │ 0 │" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "using SpatialEcology, Plots\n", + "amph = readtable(\"/Users/michael/Downloads/amphibians_PA_matrix.csv\")\n", + "amph[1:4,1:4]" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": { + "collapsed": false + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Data assumed to be a concatenation of coordinates (3 columns) and occurrence matrix\n" + ] + }, + { + "data": { + "text/plain": [] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Assemblage with 235173 records of 6110 species in 14376 sites\n", + "\n", + "Species names:\n", + "_Bufo_arabicus, _Bufo_atukoralei, _Bufo_beddomii...Zachaenus_carvalhoi, Zachaenus_parvulus\n", + "\n", + "Site names:\n", + "1, 2, 3...14375, 14376\n" + ] + } + ], + "source": [ + "amph[:WorldMapID] = [\"$i\" for i in amph[:WorldMapID]]\n", + "amph = Assemblage(amph)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Register colors and start backend" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": { + "collapsed": false + }, + "outputs": [ + { + "data": { + "text/plain": [ + "Dict{Symbol,Array{ColorTypes.RGBA{Float64},1}} with 24 entries:\n", + " :jet => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.0,0.0,0.560784,1.0)…\n", + " :parula => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.207843,0.164706,0.5…\n", + " :cube => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.454902,0.0,0.505882…\n", + " :lightrainbow => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.801961,0.3,0.801961…\n", + " :reds => ColorTypes.RGBA{Float64}[RGBA{Float64}(1.0,0.713725,0.756863…\n", + " :moreland => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.231373,0.298039,0.7…\n", + " :redblue => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.403922,0.0,0.121569…\n", + " :blues => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.678431,0.847059,0.9…\n", + " :redsblues => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.545098,0.0,0.0,1.0)…\n", + " :darkrainbow => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.401961,0.0,0.401961…\n", + " :viridis => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.267004,0.004874,0.3…\n", + " :greens => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.564706,0.933333,0.5…\n", + " :plasma => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.050383,0.029803,0.5…\n", + " :heat => ColorTypes.RGBA{Float64}[RGBA{Float64}(1.0,1.0,0.878431,1.0)…\n", + " :magma => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.001462,0.000466,0.0…\n", + " :blackbody => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.0,0.0,0.0,1.0),RGBA…\n", + " :inferno => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.001462,0.000466,0.0…\n", + " :HMrainbow => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.0,0.0,0.0,1.0),RGBA…\n", + " :rainbow => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.501961,0.0,0.501961…\n", + " :bluesreds => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.0,0.0,0.545098,1.0)…\n", + " :darktest => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.0,0.0,0.545098,1.0)…\n", + " :grays => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.95,0.95,0.95,1.0),R…\n", + " :blueyellow => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.027451,0.027451,0.9…\n", + " :lighttest => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.3,0.3,0.845098,1.0)…" + ] + }, + "execution_count": 15, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "registercolors()\n", + "plotlyjs()\n", + "PlotUtils._gradients" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Example plots" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": { + "collapsed": false + }, + "outputs": [ + { + "data": { + "text/html": [ + "\n", + "\n", + " \n", + "\n", + "\n", + "
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\n", + "\n", + "\n", + "\n", + "\n", + "\n" + ] + }, + "execution_count": 18, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "plot(amph, color = :blackbody, size = [800,400])" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "collapsed": true + }, + "outputs": [], + "source": [] + } + ], + "metadata": { + "anaconda-cloud": {}, + "kernelspec": { + "display_name": "Julia 0.5.0", + "language": "julia", + "name": "julia-0.5" + }, + "language_info": { + "file_extension": ".jl", + "mimetype": "application/julia", + "name": "julia", + "version": "0.5.0" + } + }, + "nbformat": 4, + "nbformat_minor": 1 +} diff --git a/doc/Color gradient examples.ipynb b/doc/Color gradient examples.ipynb new file mode 100644 index 0000000..8ef8789 --- /dev/null +++ b/doc/Color gradient examples.ipynb @@ -0,0 +1,485 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Example plots to show color themes included in SpatialEcology.jl\n", + "To use the themes when plotting with Plots.jl, simply call `registercolors()`, and the gradients become available " + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Loading data\n", + "For this example we use the global species richness pattern of amphibians, based on data from IUCN." + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": { + "collapsed": false + }, + "outputs": [ + { + "data": { + "text/html": [ + "
LongLatWorldMapID_Bufo_arabicus
1-72.5-54.5519480
2-71.5-54.5519490
3-70.5-54.5519500
4-74.5-53.5515860
" + ], + "text/plain": [ + "4×4 DataFrames.DataFrame\n", + "│ Row │ Long │ Lat │ WorldMapID │ _Bufo_arabicus │\n", + "├─────┼───────┼───────┼────────────┼────────────────┤\n", + "│ 1 │ -72.5 │ -54.5 │ 51948 │ 0 │\n", + "│ 2 │ -71.5 │ -54.5 │ 51949 │ 0 │\n", + "│ 3 │ -70.5 │ -54.5 │ 51950 │ 0 │\n", + "│ 4 │ -74.5 │ -53.5 │ 51586 │ 0 │" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "using SpatialEcology, Plots\n", + "amph = readtable(\"/Users/michael/Downloads/amphibians_PA_matrix.csv\")\n", + "amph[1:4,1:4]" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": { + "collapsed": false + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Data assumed to be a concatenation of coordinates (3 columns) and occurrence matrix\n" + ] + }, + { + "data": { + "text/plain": [] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Assemblage with 235173 records of 6110 species in 14376 sites\n", + "\n", + "Species names:\n", + "_Bufo_arabicus, _Bufo_atukoralei, _Bufo_beddomii...Zachaenus_carvalhoi, Zachaenus_parvulus\n", + "\n", + "Site names:\n", + "1, 2, 3...14375, 14376\n" + ] + } + ], + "source": [ + "amph[:WorldMapID] = [\"$i\" for i in amph[:WorldMapID]]\n", + "amph = Assemblage(amph)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Register colors and start backend" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": { + "collapsed": false + }, + "outputs": [ + { + "data": { + "text/plain": [ + "Dict{Symbol,Array{ColorTypes.RGBA{Float64},1}} with 24 entries:\n", + " :jet => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.0,0.0,0.560784,1.0)…\n", + " :parula => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.207843,0.164706,0.5…\n", + " :cube => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.454902,0.0,0.505882…\n", + " :lightrainbow => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.801961,0.3,0.801961…\n", + " :reds => ColorTypes.RGBA{Float64}[RGBA{Float64}(1.0,0.713725,0.756863…\n", + " :moreland => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.231373,0.298039,0.7…\n", + " :redblue => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.403922,0.0,0.121569…\n", + " :blues => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.678431,0.847059,0.9…\n", + " :redsblues => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.545098,0.0,0.0,1.0)…\n", + " :darkrainbow => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.401961,0.0,0.401961…\n", + " :viridis => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.267004,0.004874,0.3…\n", + " :greens => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.564706,0.933333,0.5…\n", + " :plasma => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.050383,0.029803,0.5…\n", + " :heat => ColorTypes.RGBA{Float64}[RGBA{Float64}(1.0,1.0,0.878431,1.0)…\n", + " :magma => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.001462,0.000466,0.0…\n", + " :blackbody => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.0,0.0,0.0,1.0),RGBA…\n", + " :inferno => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.001462,0.000466,0.0…\n", + " :HMrainbow => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.0,0.0,0.0,1.0),RGBA…\n", + " :rainbow => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.501961,0.0,0.501961…\n", + " :bluesreds => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.0,0.0,0.545098,1.0)…\n", + " :darktest => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.0,0.0,0.545098,1.0)…\n", + " :grays => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.95,0.95,0.95,1.0),R…\n", + " :blueyellow => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.027451,0.027451,0.9…\n", + " :lighttest => ColorTypes.RGBA{Float64}[RGBA{Float64}(0.3,0.3,0.845098,1.0)…" + ] + }, + "execution_count": 15, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "registercolors()\n", + "plotlyjs()\n", + "PlotUtils._gradients" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Example plots" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": { + "collapsed": false + }, + "outputs": [ + { + "data": { + "text/html": [ + "\n", + "\n", + " \n", + "\n", + "\n", + "
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