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script.r
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script.r
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# Copyright (c) Microsoft Corporation. All rights reserved.
# Third Party Programs. This software enables you to obtain software applications from other sources.
# Those applications are offered and distributed by third parties under their own license terms.
# Microsoft is not developing, distributing or licensing those applications to you, but instead,
# as a convenience, enables you to use this software to obtain those applications directly from
# the application providers.
# By using the software, you acknowledge and agree that you are obtaining the applications directly
# from the third party providers and under separate license terms, and that it is your responsibility to locate,
# understand and comply with those license terms.
# Microsoft grants you no license rights for third-party software or applications that is obtained using this software.
##PBI_R_VISUAL: VIZGAL_CORRPLOT Graphical display of a correlation matrix.
# Computes and visualizes a correlation matrix. Used to investigate the
# dependency between multiple variables at the same time. It also contains some algorithms
# to do matrix reordering and grouping of variables.
# INPUT:
# The input dataset should include at least two numerical non-constant columns
#
# EXAMPLES:
# #for R environment
# dataset<-mtcars #assign dataset
# source("visGal_corrplot.R") #create graphics
#
# WARNINGS:
#
# CREATION DATE: 06/01/2016
#
# LAST UPDATE: 07/26/2016
#
# VERSION: 0.0.1
#
# R VERSION TESTED: 3.2.2
#
# AUTHOR: pbicvsupport@microsoft.com
#
# REFERENCES: https://cran.r-project.org/web/packages/corrplot/vignettes/corrplot-intro.html
#save(list = ls(all.names = TRUE), file='C:/Users/boefraty/projects/PBI/R/tempData.Rda')
#load(file='C:/Users/boefraty/projects/PBI/R/tempData.Rda')
cutStr2Show = function(strText, strCex = 0.8, abbrTo = 100, isH = TRUE, maxChar = 0, partAvailable = 1)
{
# strText = text to modify
# strCex = font size
# abbrTo = very long string will be abbreviated to "abbrTo" characters
# isH = "is horizontal" ?
# maxChar = text smaller than maxChar is replaced by NULL
# partAvailable = which portion of window is available for text, in [0,1]
if(is.null(strText))
return (NULL)
SCL = 0.094*strCex
pardin = par()$din
gStand = partAvailable*(isH*pardin[1]+(1-isH)*pardin[2]) /SCL
# if very very long abbreviate
if(nchar(strText)>abbrTo && nchar(strText)> 1)
strText = abbreviate(strText, abbrTo)
# if looooooong convert to lo...
if(nchar(strText)>round(gStand) && nchar(strText)> 1)
strText = paste(substring(strText,1,floor(gStand)),"...",sep="")
# if shorter than maxChar remove
if(gStand<=maxChar)
strText = NULL
return(strText)
}
verifyIfToShowCoeff = function(numR, numDigs, coeffCex, partAvailble = 0.75)
{
myThre = 0.1
lenPerD = partAvailble*min(par()$din)/(numR*(numDigs+1)*coeffCex)
return(lenPerD>myThre)
}
verifyIfToShowColorScale = function(numR, partAvailble = 0.05)
{
myThre = 0.02
lenPerD = partAvailble*par()$din[1]/(numR)
return(lenPerD>myThre)
}
getValueNumericMinMaxDefault = function(val,minVal = -Inf,maxVal = Inf,defVal = NA)
{
if(!is.numeric(val) && !is.na(defVal))
val = defVal
if(val<minVal)
val = minVal
if(val>maxVal)
val = maxVal
return(val)
}
if(!exists("dataset") && exists("Values"))
dataset = Values
#PBI_EXAMPLE_DATASET for debugging purposes
if(!exists("dataset"))
{
require("datasets")
dataset=data.frame(mtcars) #mpg,cyl,disp,hp,drat,wt,qsec,vs,am,gear,carb
}
############ User Parameters #########
if(exists("settings_corrplot_params_show") && settings_corrplot_params_show == FALSE)
rm(list= ls(pattern = "settings_corrplot_params_"))
if(exists("settings_labels_params_show") && settings_labels_params_show == FALSE)
rm(list= ls(pattern = "settings_labels_params_"))
if(exists("settings_coeff_params_show") && settings_coeff_params_show == FALSE)
rm(list= ls(pattern = "settings_coeff_params_"))
#if(exists("settings_additional_params_show") && settings_additional_params_show == FALSE)
# rm(list= ls(pattern = "settings_additional_params_"))
##PBI_PARAM: Should warnings text be displayed?
#Type:logical, Default:TRUE, Range:NA, PossibleValues:NA, Remarks: NA
showWarnings = FALSE
if(exists("settings_additional_params_showWarnings"))
showWarnings = settings_additional_params_showWarnings
##PBI_PARAM: visualization method of items inside the table
#Type:string, Default:'circle', Range:NA, PossibleValues:("circle", "square", "ellipse", "number", "shade", "color", "pie"), Remarks: NA
method = 'circle'
if(exists("settings_corrplot_params_method"))
method = settings_corrplot_params_method
##PBI_PARAM: layout type, defines if we display full, lower triangular or upper triangular matrix.
#Type:string, Default:'full', Range:NA, PossibleValues:("full", "upper", "lower"), Remarks: If rectangles are added, this option is switched to "full"
type = 'full'
if(exists("settings_corrplot_params_mytype"))
type = settings_corrplot_params_mytype
##PBI_PARAM: order of raws is one of "original","hclust"(hierarchical clustering order), "alphabet", "AOE"(angular order of the eigenvectors), "FPC"( first principal component order)
#Type:string, Default:'original', Range:NA, PossibleValues:("original","hclust","alphabet", "AOE", "FPC"), Remarks: NA
order='original'
if(exists("settings_corrplot_params_order"))
order = settings_corrplot_params_order
##PBI_PARAM: number of clusters to be drawn on top of correlation matrix as rectangles
#if order is "hclust" and type is "full" visual will draw rectangles around the correlation matrix
# addrect can also be integer or NULL (add nothing) or NaN (auto)
#Type:unsigned integer, Default:NaN, Range:NA, PossibleValues:NA, Remarks: If equals NaN, will find number automatically
addrect= 0
if(exists("settings_corrplot_params_addrect"))
{
addrect = as.numeric(settings_corrplot_params_addrect)
if(is.na(addrect) || addrect>1)
{
order='hclust'
type = 'full'
}
}
###############Library Declarations###############
libraryRequireInstall = function(packageName, ...)
{
if(!require(packageName, character.only = TRUE))
warning(paste("*** The package: '", packageName, "' was not installed ***",sep=""))
}
libraryRequireInstall("corrplot")
###############Internal parameters definitions#################
##PBI_PARAM: color of text label
#Type:string, Default:'orange', Range:NA, PossibleValues:("red","black","green", "blue", "gray"),
#Remarks: see colors() function for full list of built-in color names
tl.col = "red"
if(exists("settings_labels_params_tl_col"))
tl.col = settings_labels_params_tl_col
##PBI_PARAM: font size of text label
#Type:numeric, Default:0.9, Range:(0,Inf], PossibleValues:NA,
#Remarks: NA
tl.cex = 1
if(exists("settings_labels_params_textSize"))
tl.cex = as.numeric(settings_labels_params_textSize)/10
##PBI_PARAM: Color of coefficients added on the graph. If NULL (default), add no coefficients
#Type:string, Default:NULL, Range:NA, PossibleValues:("white","black","green","gray",NULL),
#Remarks: NA
addCoef.col = NA
if(exists("settings_coeff_params_addCoef_col"))
addCoef.col = (settings_coeff_params_addCoef_col)
##PBI_PARAM: size of coefficients added on the graph.
#Type:numeric, Default:0.6, Range:[0,1], PossibleValues:NA,
#Remarks: NA
number.cex = 0.8
if(exists("settings_coeff_params_textSize"))
number.cex = as.numeric(settings_coeff_params_textSize)/10
##PBI_PARAM: the number of decimal digits to be added into the plot
#Type:numeric, Default:1, Range:[1,3], PossibleValues:NA,
#Remarks: NA
number.digits = 1*as.numeric(exists("settings_coeff_params_show"))
## Do not touch ##
#back <- "#1a1a1a"
if(exists("backgroundColorParam_color")) back = backgroundColorParam_color else back = "#1a1a1a"
#back = backgroundColorParam_color
if(exists("settings_coeff_params_number_digits"))
{
number.digits = as.numeric(settings_coeff_params_number_digits)
if(is.na(number.digits))
{
addCoef.col = NULL
number.digits = 0
}
}
if(number.digits == 0)
addCoef.col = NULL
##PBI_PARAM: the default margin definition of the plot
#Type:vector, Default:c(1.0, 0.75, 0.75, 0.6), Range:NA, PossibleValues:NA,
#Remarks: NA
defMar = c(0,0,0,0)
MAX_CHAR_TL = 50 # maximum characters for text label
MAX_PART_TL = 0.5 # maximum space for text label
clpos = "r" #location of color scale
###############Internal functions definitions#################
#by default will group variables in log of number of columns clusters
autoDetectAddrect <- function(dataset) { ceiling(log(ncol(dataset))) }
#verify if the column is numeric and non-constant
correctColumn <- function(someColumn) { is.numeric(someColumn) && length(unique(someColumn)) > 1 }
###############Upfront input correctness validations (where possible)#################
pbiWarning <- NULL
#PBI_COMMENT: verify correctness of dataset
useColumns <- sapply(dataset,correctColumn)
if(showWarnings && sum(useColumns) < ncol(dataset))
pbiWarning <- "Some columns are not numeric, or constant."
dataset <- as.data.frame(dataset[,useColumns])
nc <- ncol(dataset)
nr <- nrow(dataset)
nnn = names(dataset)
nnn1 = sapply(nnn,cutStr2Show, strCex = tl.cex, abbrTo = MAX_CHAR_TL, isH = (par()$din[1]<par()$din[2]), maxChar = 2, partAvailable = MAX_PART_TL)
names(dataset) = nnn1
#PBI_COMMENT: re-define addrect to avoid errors in input
if(!is.null(addrect))
{
if((is.na(addrect)||!is.numeric(addrect)||addrect < 0) && !is.null(nc))
addrect=autoDetectAddrect(dataset)
addrect <- max(1, min(round(addrect), nc))
if(order == 'hclust' && addrect > 1) #enable adding rectangle by type=full
type <- 'full'
}
##############Main Visualization script###########
if(!is.null(addCoef.col))
if(!verifyIfToShowCoeff(nc, number.digits, number.cex, partAvailble = 0.75))
{
addCoef.col = NULL
pbiWarning<-paste(pbiWarning, "Not enough space for coefficients.", sep=" ")
}
if(!verifyIfToShowColorScale(nc))
clpos = "n"
#PBI_COMMENT: Create visual
if(nc > 1 && nr > 1){
#PBI_COMMENT: compute correlation matrix, allow for missing values
M <- cor(dataset, use="pairwise.complete.obs")
par(xpd = TRUE )
if(type == "upper")
{
defMar = c(0.25, 0.25, 0.25, 0.1) + 0.5
tl.cex = tl.cex*0.95
}
filetag <- "corrplot_result.png"
#png(filetag, color="#00FF00")
par(xpd = TRUE, bg = back)
corrplot(M, method=method, order=order, type=type, addrect=addrect,
tl.col = tl.col, tl.cex=tl.cex,
number.digits=number.digits, number.cex=number.cex, addCoef.col=addCoef.col,
cl.pos =clpos, bg=back)
usr <- par("usr")
plot.new()
par(usr=usr)
corrplot(M, method=method, order=order, type=type, addrect=addrect,
tl.col = tl.col, tl.cex=tl.cex,
number.digits=number.digits, number.cex=number.cex, addCoef.col=addCoef.col,
cl.pos ='r', tl.srt = 45, bg=back, add=TRUE)
}else{ #empty correlation plot
plot.new()
pbiWarning<-paste(pbiWarning, "Not enough input dimensions.", sep=" ")
}
#add warning as subtitle
if(showWarnings)
{
pbiWarning <- cutStr2Show(pbiWarning,strCex = 0.8, abbrTo = 100, isH = TRUE)
title(main = NULL, sub = pbiWarning, outer = FALSE, col.sub = "red", cex.sub = 0.5)
}