Hands-on_Ex05_2

Author

YIN HANG

Published

February 11, 2023

Heatmap

Install and Launch R Packages using pacman

pacman::p_load(seriation, dendextend, heatmaply, tidyverse, GGally, parallelPlot)

wh <- read_csv("data/WHData-2018.csv")

Rows: 156 Columns: 12
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr  (2): Country, Region
dbl (10): Happiness score, Whisker-high, Whisker-low, Dystopia, GDP per capi...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

Change row number by country name

row.names(wh) <- wh$Country

Warning: Setting row names on a tibble is deprecated.

Transform data frame into matrix

wh1 <- dplyr::select(wh, c(3, 7:12))
wh_matrix <- data.matrix(wh)

Heatmap() of R Stats

wh_heatmap <- heatmap(wh_matrix,
                      Rowv=NA, Colv=NA)

Plot a cluster heatmap

wh_heatmap <- heatmap(wh_matrix)

Normalise matric column-wise

wh_heatmap <- heatmap(wh_matrix,
                      scale="column",
                      cexRow = 0.6, 
                      cexCol = 0.8,
                      margins = c(10, 4))

Create Interactive heatmap

There are a few ways to transform the data.

There are scaling method, normalising method and percentage method

heatmaply(wh_matrix[,-c(1,2,4,5)],
          scale = "column")

Warning in doTryCatch(return(expr), name, parentenv, handler): unable to load shared object '/Library/Frameworks/R.framework/Resources/modules//R_X11.so':
  dlopen(/Library/Frameworks/R.framework/Resources/modules//R_X11.so, 0x0006): Library not loaded: '/opt/X11/lib/libSM.6.dylib'
  Referenced from: '/Library/Frameworks/R.framework/Versions/4.2/Resources/modules/R_X11.so'
  Reason: tried: '/opt/X11/lib/libSM.6.dylib' (no such file), '/Library/Frameworks/R.framework/Resources/lib/libSM.6.dylib' (no such file), '/Library/Java/JavaVirtualMachines/jdk1.8.0_241.jdk/Contents/Home/jre/lib/server/libSM.6.dylib' (no such file)

heatmaply(normalize(wh_matrix[,-c(1,2,4,5)]))

heatmaply(percentize(wh_matrix[, -c(1, 2, 4, 5)]))

Further spread out

heatmaply(normalize(wh_matrix[, -c(1, 2, 4, 5)]),
          Colv=NA,
          seriate = "none",
          colors = Blues,
          k_row = 5,
          margins = c(NA,200,60,NA),
          fontsize_row = 4,
          fontsize_col = 5,
          main="World Happiness Score and Variables by Country, 2018 \nDataTransformation using Normalise Method",
          xlab = "World Happiness Indicators",
          ylab = "World Countries"
          )

Plot Static Parallel Coordinate

ggparcoord(data = wh, 
           columns = c(7:12))

Plot Parallel coordinates with boxplot

ggparcoord(data = wh, 
           columns = c(7:12), 
           groupColumn = 2,
           scale = "uniminmax",
           alphaLines = 0.2,
           boxplot = TRUE, 
           title = "Parallel Coordinates Plot of World Happines Variables")

Warning: The following aesthetics were dropped during statistical transformation: colour
ℹ This can happen when ggplot fails to infer the correct grouping structure in
  the data.
ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
  variable into a factor?