cmplot_julia_with_examples.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## <center>Cloudy Mountain Plot<br>an informative RDI<i>(*)</i> categorical distribution plot<br>inspired by Violin, Bean and Pirate Plots</center>\n",
    "#### <center>云山图 [yún shān tú] / 雲山図 [くもやまず/kumo yama zu]</center>\n",
    "### by [Dr Giuseppe Insana](http://insana.net), August 2019 - coded in Julia and Python\n",
    "#### <i>(*)</i>: RDI = Raw data + Descriptive statistics + Inferential statistics"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### This notebook shows usage examples of Cloudy Mountain Plot in Julia.\n",
    "### Please check the [CMPlot.jl github page](https://github.com/g-insana/CMPlot.jl) for installation instruction and options"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "hideCode": false,
    "hidePrompt": false
   },
   "outputs": [],
   "source": [
    "using CMPlot\n",
    "using PlotlyJS\n",
    "using Random #for shuffle()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "hideCode": false,
    "hidePrompt": false
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   "outputs": [],
   "source": [
    "#To load some public test data:\n",
    "using RDatasets\n",
    "iris = dataset(\"datasets\", \"iris\") # Iris dataset; Anderson, Edgar (1935) Fisher, R. A. (1936) ; http://vincentarelbundock.github.io/Rdatasets/doc/datasets/iris.html\n",
    "train = dataset(\"Ecdat\", \"Wages\") # Individual wages, US, 1976 to 1982; Cornwell, C. and P. Rupert (1988) ; http://vincentarelbundock.github.io/Rdatasets/doc/Ecdat/Wages.html\n",
    "train[!,:ExpYears]=[if x < 10 \"<10\" elseif x >= 10 && x < 30 \"10-29\" else \">30\" end for x in train.Exp] #binning on years of full-time work experience\n",
    "train[!,:EduYears]=[if x < 9 \"<9\" elseif x >= 9 && x < 14 \"9-13\" else \">13\" end for x in train.Ed] #binning on years of education\n",
    "train = train[shuffle(1:size(train, 1)),:] #shuffle if you wish to bias when using pointsmaxdisplayed\n",
    "train[1:3,:]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#Alternatively, load your own data, e.g. via CSV:\n",
    "#=\n",
    "using CSV\n",
    "using Statistics\n",
    "train = DataFrame(CSV.File(\"train.csv\", delim=',', decimal='.')) #dataset on loans\n",
    "#Some data cleaning:\n",
    "train.Married=coalesce.(train.Married,\"No\") #replace missing values in Married with \"No\"\n",
    "train.Gender=coalesce.(train.Gender,\"Male\") #replace missing values in Gender with \"Male\"\n",
    "train.LoanAmount=coalesce.(train.LoanAmount,floor(Int,mean(skipmissing(train.LoanAmount)))) #replace missing values in LoanAmount with their mean\n",
    "train.LoanAmount[1]\n",
    "=#"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 1 min Quickstart: just pass as arguments a dataframe and the column label for the categorical data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "plot(cmplot(iris,xcol=:Species)...) #using splat operator"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## A little evolutionary history, via box plots and violins:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "hideCode": false,
    "hidePrompt": false
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   "source": [
    "using PlotlyJS\n",
    "layout=Layout(\n",
    "        title=\"BoxPlot\",xaxis_title=\"Wage (log)\",yaxis_title=\"Married+Gender\",\n",
    "        xaxis_showgrid=true, yaxis_showgrid=true,\n",
    "        margin_t=20,\n",
    "        legend_y=0.9, legend_x=0.8,\n",
    "        )\n",
    "\n",
    "boxbygender=box(y=train.Sex, x=train.LWage, name=\"Gender\",legendgroup=\"gender\",orientation=\"h\",marker_color=\"green\")\n",
    "boxbymarried=box(y=train.Married, x=train.LWage, name=\"Married\",legendgroup=\"married\",orientation=\"h\",marker_color=\"blue\")\n",
    "violbygender=violin(y=train.Sex, x=train.LWage, name=\"Gender\",legendgroup=\"gender\",box_visible=true,\n",
    "    orientation=\"h\",marker_color=\"green\")\n",
    "violbymarried=violin(y=train.Married, x=train.LWage, name=\"Married\",legendgroup=\"married\",box_visible=true,\n",
    "    orientation=\"h\",marker_color=\"blue\")\n",
    "p1=PlotlyJS.plot([boxbygender,boxbymarried],layout)\n",
    "#savefig(p1::Union{Plot,PlotlyJS.SyncPlot}, joinpath(homedir(),\"married_plus_gender-loanamount_boxplot.pdf\"))\n",
    "\n",
    "layout[\"title\"]=\"ViolinPlot\"\n",
    "layout[\"yaxis_title\"]=\" \"\n",
    "p2=PlotlyJS.plot([violbygender,violbymarried],layout)#,style=mystyle)\n",
    "#savefig(p2::Union{Plot,PlotlyJS.SyncPlot}, joinpath(homedir(),\"married_plus_gender-loanamount_violinplot.pdf\"))\n",
    "[p1 p2]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### And this would be same data shown using bean plots and pirate plots:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "(bt1,layout)=cmplot(train; xcol=:Sex, ycol=:LWage, orientation=\"h\",inf=\"none\",ycolorgroups=false,\n",
    "    side=\"both\",colorshift=2,colorrange=4,pointsopacity=1,showpoints=true,showboxplot=false,pointshapes=[\"line-ns\"],\n",
    "    markoutliers=false,pointsmaxdisplayed=200)\n",
    "(bt2,layout)=cmplot(train; xcol=:Married, ycol=:LWage, orientation=\"h\",inf=\"none\",ycolorgroups=false,\n",
    "    side=\"both\",colorshift=0,colorrange=4,pointsopacity=1,showpoints=true,showboxplot=false,pointshapes=[\"line-ns\"],\n",
    "    markoutliers=false,pointsmaxdisplayed=200)\n",
    "layout[\"title\"]=\"BeanPlot\"\n",
    "layout[\"yaxis_title\"]=\"Married + Gender\"\n",
    "layout[\"xaxis_title\"]=\"Wage (log)\"\n",
    "layout[\"margin_t\"]=30\n",
    "layout[\"showlegend\"]=false\n",
    "\n",
    "p1=PlotlyJS.plot(union(bt1,bt2),layout)\n",
    "#savefig(p1::Union{Plot,PlotlyJS.SyncPlot}, joinpath(homedir(),\"married_plus_gender-loanamount_rdiplot.pdf\"))\n",
    "\n",
    "#union of two different Xcolumns, joining pirate plot like traces:\n",
    "(pt1,layout)=cmplot(train; xcol=:Sex, ycol=:LWage, orientation=\"h\",inf=\"hdi\",ycolorgroups=false,\n",
    "    side=\"both\",colorshift=2,colorrange=4,pointsopacity=0.3,showpoints=true,showboxplot=false,pointshapes=[\"circle\"],\n",
    "    markoutliers=false,pointsmaxdisplayed=200)\n",
    "(pt2,layout)=cmplot(train; xcol=:Married, ycol=:LWage, orientation=\"h\",inf=\"hdi\",ycolorgroups=false,\n",
    "    side=\"both\",colorshift=0,colorrange=4,pointsopacity=0.3,showpoints=true,showboxplot=false,pointshapes=[\"circle\"],\n",
    "    markoutliers=false,pointsmaxdisplayed=200)\n",
    "layout[\"title\"]=\"PiratePlot\"\n",
    "layout[\"yaxis_title\"]=\" \"\n",
    "layout[\"xaxis_title\"]=\"Wage (log)\"\n",
    "layout[\"margin_t\"]=30\n",
    "layout[\"legend\"]=attr(orientation=\"h\")\n",
    "\n",
    "p2=PlotlyJS.plot(union(pt1,pt2),layout)\n",
    "#savefig(p2::Union{Plot,PlotlyJS.SyncPlot}, joinpath(homedir(),\"married_plus_gender-loanamount_pirateplot.pdf\"))\n",
    "[p1 p2]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Until we arrive to the cloudy mountain plots:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# union of two separate Xcolumns (Gender + Married)\n",
    "(traces1,layout)=cmplot(train; xcol=:Sex, ycol=:LWage, xsuperimposed=false,orientation=\"h\",\n",
    "    colorshift=2,colorrange=4,ycolorgroups=false,side=\"pos\",inf=\"hdi\",conf_level=0.95,altsidesflip=false,\n",
    "    pointsoverdens=true,showpoints=true,pointshapes=[\"triangle-down\",\"triangle-up\"],pointsopacity=0.2,\n",
    "    pointsdistance=1,pointsmaxdisplayed=400)\n",
    "(traces2,layout)=cmplot(train; xcol=:Married, ycol=:LWage, xsuperimposed=false,\n",
    "    orientation=\"h\",colorshift=0,colorrange=4,ycolorgroups=false,side=\"pos\",inf=\"hdi\",conf_level=0.95,\n",
    "    altsidesflip=false,pointsoverdens=true,showpoints=true,pointshapes=[\"triangle-right\",\"triangle-left\"],\n",
    "    pointsopacity=0.3,pointsdistance=1,pointsmaxdisplayed=400,title=\"CloudyMountainPlot\")\n",
    "layout[\"legend_tracegroupgap\"]=0\n",
    "layout[\"xaxis_title\"]=\"Wage (log)\"\n",
    "layout[\"yaxis_title\"]=\"Married and Gender\"\n",
    "layout[\"margin_l\"]=60\n",
    "#layout[\"yaxis_range\"]=[-0.1,3.51]\n",
    "p1=plot(union(traces1,traces2),layout)\n",
    "#savefig(p1::Union{Plot,PlotlyJS.SyncPlot}, joinpath(homedir(),\"married_plus_gender-loanamount_overimposed_rdiplot.pdf\"))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### ... which is particularly powerful when overimposed for same X:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Superimposed rdi plots for union of two separate Xcolumns (Gender + Married)\n",
    "(traces1,layout)=cmplot(train; xcol=:Sex, ycol=:LWage, xlabel=\"M/F\", xsuperimposed=true,orientation=\"h\",\n",
    "    colorshift=2,colorrange=4,ycolorgroups=false,side=\"alt\",inf=\"hdi\",conf_level=0.95,altsidesflip=false,\n",
    "    pointsoverdens=true,showpoints=true,pointshapes=[\"triangle-down\",\"triangle-up\"],pointsdistance=0.6,\n",
    "    pointsmaxdisplayed=400)\n",
    "(traces2,layout)=cmplot(train; xcol=:Married, ycol=:LWage, xlabel=\"married?\", xsuperimposed=true,\n",
    "    orientation=\"h\",colorshift=0,colorrange=4,ycolorgroups=false,side=\"alt\",inf=\"hdi\",conf_level=0.95,\n",
    "    altsidesflip=false,pointsoverdens=true,showpoints=true,pointshapes=[\"triangle-right\",\"triangle-left\"]\n",
    "    ,pointsdistance=0.6,pointsmaxdisplayed=400)\n",
    "layout[\"legend_tracegroupgap\"]=0\n",
    "layout[\"yaxis_title\"]=\"Married and Gender\"\n",
    "layout[\"xaxis_title\"]=\"Wage (log)\"\n",
    "layout[\"title\"]=\"Married + Gender ~ Wage\"\n",
    "layout[\"margin_l\"]=60\n",
    "#layout[\"yaxis_range\"]=[-0.51,1.51]\n",
    "p1=plot(union(traces1,traces2),layout)\n",
    "#savefig(p1::Union{Plot,PlotlyJS.SyncPlot}, joinpath(homedir(),\"married_plus_gender-loanamount_overimposed_rdiplot.pdf\"))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Now some illustrative usage examples\n",
    "### First: two Ycol side by side\n",
    "#### (notice the raw point \"clouds\" on opposite side of the kernel density \"mountains\", for better clarity)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#IRIS dataset, plotting two Ycol side by side\n",
    "traces,layout=cmplot(iris,xcol=:Species,ycol=[:SepalLength,:PetalLength],\n",
    "    colorrange=3,pointshapes=[\"star-triangle-up\",\"star-diamond\",\"star-square\"])\n",
    "p1=plot(traces,layout)\n",
    "#savefig(p1::Union{Plot,PlotlyJS.SyncPlot}, joinpath(homedir(),\"species-sepallength_petallength_rdiplot.pdf\"))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### It works well also with three Ycol:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#IRIS dataset, plotting three Ycol side by side\n",
    "traces,layout=cmplot(iris,xcol=:Species,ycol=[:SepalLength,:PetalLength,:SepalWidth],\n",
    "    pointshapes=[\"star-triangle-up\",\"star-diamond\",\"star-square\"])\n",
    "p1=plot(traces,layout)\n",
    "\n",
    "#savefig(p1::Union{Plot,PlotlyJS.SyncPlot}, joinpath(homedir(),\"species-sepallength_petallength_sepalwidth_rdiplot.pdf\"))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Excursus: not only we can show different Xcol together, but we can intersect them, grouping the data by two or more X\n",
    "### For example, combining two X a different picture is revealed:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#intersection of two different Xcolumns:\n",
    "traces,layout=cmplot(train; xcol=[:Married,:Sex], ycol=:LWage,ycolorgroups=false,\n",
    "    side=\"pos\",pointshapes=[\"star-diamond\"],pointsmaxdisplayed=500)\n",
    "layout[\"legend_tracegroupgap\"]=0\n",
    "layout[\"title\"]=\"Married & Gender ~ Wage\"\n",
    "layout[\"yaxis_title\"]=\"Married & Gender\"\n",
    "layout[\"xaxis_title\"]=\"Wage (log)\"\n",
    "p1=plot(traces,layout)\n",
    "#savefig(p1::Union{Plot,PlotlyJS.SyncPlot}, joinpath(homedir(),\"married_gender-loanamount_rdiplot.pdf\"))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Or with three:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#intersection of three different Xcolumns:\n",
    "traces,layout=cmplot(train; xcol=[:Sex,:Married,:SMSA], ycol=:LWage, ycolorgroups=false, side=\"both\",\n",
    "    pointsmaxdisplayed=300)\n",
    "layout[\"legend_tracegroupgap\"]=0\n",
    "layout[\"margin_l\"]=180\n",
    "layout[\"margin_r\"]=0\n",
    "layout[\"title\"]=\"Gender & Married & LivesInCity ~ Wage\"\n",
    "layout[\"yaxis_title\"]=\"Gender & Married & LivesInCity\"\n",
    "layout[\"xaxis_title\"]=\"Wage (log)\"\n",
    "p1=plot(traces,layout)\n",
    "#savefig(p1::Union{Plot,PlotlyJS.SyncPlot}, joinpath(homedir(),\"married_gender_education-applicantincome_rdiplot.pdf\"))\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Super imposition of distributions: one of the best features of cloudy mountain plots"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "hideCode": false,
    "hidePrompt": false
   },
   "outputs": [],
   "source": [
    "#Superimposed plots for a single Xcolumn\n",
    "(traces1,layout)=cmplot(train; xcol=:South, ycol=:LWage, xsuperimposed=true, pointsoverdens=true,\n",
    "    ycolorgroups=false,altsidesflip=false, colorshift=2, colorrange=4, pointshapes=[\"star\",\"pentagon\"],\n",
    "    pointsmaxdisplayed=400)\n",
    "layout[\"legend_tracegroupgap\"]=0\n",
    "layout[\"margin_b\"]=50\n",
    "layout[\"title\"]=\"South ~ Wage\"\n",
    "layout[\"xaxis_title\"]=\"Wage (log)\"\n",
    "layout[\"yaxis_title\"]=\"Resides in the south?\"\n",
    "layout[\"yaxis_range\"]=[-0.51,0.51]\n",
    "p1=plot(traces1,layout)\n",
    "#savefig(p1::Union{Plot,PlotlyJS.SyncPlot}, joinpath(homedir(),\"gender-loanamount_rdiplot.pdf\"))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#superimposed plot for combination of two X variables\n",
    "traces,layout=cmplot(train,xcol=[:Sex,:BlueCol],xsuperimposed=true,ycol=:LWage,\n",
    "    ycolorgroups=false,pointsoverdens=true,markoutliers=false,pointshapes=[\"hexagon\"],pointsmaxdisplayed=500)\n",
    "layout[\"legend_tracegroupgap\"]=0\n",
    "layout[\"title\"]=\"Gender & BlueCollar ~ Wage\"\n",
    "layout[\"xaxis_title\"]=\"Wage (log)\"\n",
    "layout[\"yaxis_title\"]=\"Gender & BlueCollar\"\n",
    "p1=plot(traces,layout)\n",
    "#savefig(p1::Union{Plot,PlotlyJS.SyncPlot}, joinpath(homedir(),\"propertyarea_gender-loanamount_rdiplot.pdf\"))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "hidePrompt": true
   },
   "outputs": [],
   "source": [
    "#superimposed plot for combination of two X variables, one of which with 3 bins\n",
    "traces,layout=cmplot(train,xcol=[:EduYears,:Union],xsuperimposed=true,ycol=:LWage,\n",
    "    ycolorgroups=false, altsidesflip=true, pointsoverdens=true,markoutliers=false,\n",
    "    pointshapes=[\"hexagon\"],pointsmaxdisplayed=100)\n",
    "layout[\"legend_tracegroupgap\"]=0\n",
    "layout[\"title\"]=\"EducationYears & UnionContract ~ Wage\"\n",
    "layout[\"xaxis_title\"]=\"Wage (log)\"\n",
    "layout[\"yaxis_title\"]=\"EducationYears & UnionContract\"\n",
    "p1=plot(traces,layout)\n",
    "#savefig(p1::Union{Plot,PlotlyJS.SyncPlot}, joinpath(homedir(),\"propertyarea_gender-loanamount_rdiplot.pdf\"))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## To save publication ready vector graphic files (e.g. svg or pdf):"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "hideCode": false,
    "hidePrompt": true
   },
   "outputs": [],
   "source": [
    "#To save the plot as high quality file:\n",
    "\n",
    "#=\n",
    "using ORCA\n",
    "savefig(p1::Union{Plot,PlotlyJS.SyncPlot}, joinpath(homedir(),\"output_filename.svg\"))\n",
    "savefig(p1::Union{Plot,PlotlyJS.SyncPlot}, joinpath(homedir(),\"output_filename.pdf\"))\n",
    "=#\n",
    "\n",
    "#NOTE: if it does not work, try from a terminal to manually start the conda server, \n",
    "#      e.g. \"conda run orca serve -p 7982\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## To save a plot as standalone html:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "jsonplot1 = json(p1)\n",
    "template = \"<html>\n",
    "<head>\n",
    "    <script src='https://cdn.plot.ly/plotly-latest.min.js'></script>\n",
    "</head>\n",
    "<body>\n",
    "    <div id='divPlotly'></div>\n",
    "    <script>\n",
    "        var plotly_data = $jsonplot1\n",
    "        Plotly.react('divPlotly', plotly_data.data, plotly_data.layout);\n",
    "    </script>\n",
    "</body>\n",
    "\n",
    "</html>\"\n",
    "outputfilename=\"plot_name.html\"\n",
    "#=\n",
    "open(joinpath(homedir(),outputfilename), \"w\") do f\n",
    "    write(f, template)\n",
    "end\n",
    "=#"
   ]
  }
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