Make a Heatmap Table using ztable

Keon-Woong Moon

2018-07-23

Installation

You can install R package “ztable” from CRAN. Current version is 0.1.8.

install.packages("ztable")

To make a heatmap table, you have to install the developmental version of ztable from github. Current github version is 0.2.0.

if(!require(devtools)) install.packages("devtools")
devtools::install_github("cardiomoon/ztable")

Introduction

A heat map (or heatmap) is a graphical representation of data where the individual values contained in a matrix are represented as colors. You can summarize the the diagnosis and smoking status of 857 patients of acute coronary syndrome(acs) using table() function.

require(moonBook)
x=table(acs$Dx,acs$smoking)
x
                 
                  Ex-smoker Never Smoker
  NSTEMI                 42    50     61
  STEMI                  66    97    141
  Unstable Angina        96   185    119

Basic Table

You can make html or LaTex table easly with ztable.

library(ztable)
library(magrittr)
options(ztable.type="html")
z=ztable(x) 
print(z,caption="Table 1. Basic Table")
Table 1. Basic Table
  Ex-smoker Never Smoker
NSTEMI 42 50 61
STEMI 66 97 141
Unstable Angina 96 185 119

Formatting the Table

You can change the background color and font color of ztable using addCellColor function. For example, you can change the cell color of the 3rd row, 2nd column. Please keep in mind that the ztable count colname and rowname.

z %>% 
    addCellColor(4,3,bg="orange",color="white") %>% 
    print(caption="Table 2. Add Cell Color")
Table 2. Add Cell Color
  Ex-smoker Never Smoker
NSTEMI 42 50 61
STEMI 66 97 141
Unstable Angina 96 185 119

Conditional Formatting

You can select rows with logical expression. You can select cols with column name.

ztable(head(iris),caption="Table 3. Conditinoal Formatting: Sepal.Width >= 3.5") %>%
    addRowColor(rows=1,bg="#C90000",color="white") %>%
    addCellColor(condition=Sepal.Width>=3.5,cols=Sepal.Width,color="red")
Table 3. Conditinoal Formatting: Sepal.Width >= 3.5
  Sepal.Length Sepal.Width Petal.Length Petal.Width Species
1 5.10 3.50 1.40 0.20 setosa
2 4.90 3.00 1.40 0.20 setosa
3 4.70 3.20 1.30 0.20 setosa
4 4.60 3.10 1.50 0.20 setosa
5 5.00 3.60 1.40 0.20 setosa
6 5.40 3.90 1.70 0.40 setosa

Make a Heatmap Table

You can make a heatmap table in which background colors representing the values. With makeHeatmap() function, you can make a heatmap table easily. The namakeHeatmap() function apply the “Reds” palette from RColorBrewer package.

z %>% makeHeatmap() %>% print(caption="Table 4. Heatmap Table")
Table 4. Heatmap Table
  Ex-smoker Never Smoker
NSTEMI 42 50 61
STEMI 66 97 141
Unstable Angina 96 185 119

Heatmap Table with desired palette

You can change the palette with palette argument. For example, you can use the “Blue” palette.

ztable(head(mtcars)) %>% 
    makeHeatmap(palette="Blues") %>%
    print(caption="Table 5. Heatmap table with 'Blue' palette")
Table 5. Heatmap table with ‘Blue’ palette
  mpg cyl disp hp drat wt qsec vs am gear carb
Mazda RX4 21.00 6.00 160.00 110.00 3.90 2.62 16.46 0.00 1.00 4.00 4.00
Mazda RX4 Wag 21.00 6.00 160.00 110.00 3.90 2.88 17.02 0.00 1.00 4.00 4.00
Datsun 710 22.80 4.00 108.00 93.00 3.85 2.32 18.61 1.00 1.00 4.00 1.00
Hornet 4 Drive 21.40 6.00 258.00 110.00 3.08 3.21 19.44 1.00 0.00 3.00 1.00
Hornet Sportabout 18.70 8.00 360.00 175.00 3.15 3.44 17.02 0.00 0.00 3.00 2.00
Valiant 18.10 6.00 225.00 105.00 2.76 3.46 20.22 1.00 0.00 3.00 1.00

Heatmap Table with user-defined palette

With the gradientColor() function, you makes sequential colour graient palette easily.

mycolor=gradientColor(low="yellow",mid="orange",high="red",n=20,plot=TRUE)

mycolor
 [1] "#FFFF00" "#FFF500" "#FFEB00" "#FFE200" "#FFD800" "#FFCE00" "#FFC400"
 [8] "#FFBA00" "#FFAF00" "#FFA500" "#FF9B00" "#FF9000" "#FF8600" "#FF7A00"
[15] "#FF6E00" "#FF6200" "#FF5300" "#FF4300" "#FF2E00" "#FF0000"
ztable(head(mtcars[1:5])) %>% 
    makeHeatmap(mycolor=mycolor) %>%
    print(caption="Table 6. Heatmap table with user-defined palette")
Table 6. Heatmap table with user-defined palette
  mpg cyl disp hp drat
Mazda RX4 21.00 6.00 160.00 110.00 3.90
Mazda RX4 Wag 21.00 6.00 160.00 110.00 3.90
Datsun 710 22.80 4.00 108.00 93.00 3.85
Hornet 4 Drive 21.40 6.00 258.00 110.00 3.08
Hornet Sportabout 18.70 8.00 360.00 175.00 3.15
Valiant 18.10 6.00 225.00 105.00 2.76

Heatmap Table with non-numeric data

You can make heatmap table with data containing non-numeric columns. Only columns with numeric data affected by this function.

ztable(head(acs[1:10])) %>% 
    makeHeatmap %>%
    print(caption="Table 7. Heatmap table with non-numeric data")
Table 7. Heatmap table with non-numeric data
  age sex cardiogenicShock entry Dx EF height weight BMI obesity
1 62 Male No Femoral STEMI 18.00 168.00 72.00 25.51 Yes
2 78 Female No Femoral STEMI 18.40 148.00 48.00 21.91 No
3 76 Female Yes Femoral STEMI 20.00 No
4 89 Female No Femoral STEMI 21.80 165.00 50.00 18.37 No
5 56 Male No Radial NSTEMI 21.80 162.00 64.00 24.39 No
6 73 Female No Radial Unstable Angina 22.00 153.00 59.00 25.20 Yes

Selected Columnwise Heatmap Table

You can make selected columnwise heatmap table. You can select columns with cols argument. To make columnwise heatmap table, set the margin argument 2.

ztable(head(mtcars)) %>% 
    makeHeatmap(palette="YlOrRd",cols=c(1,3,4),margin=2) %>%
    print(caption="Table 8. Columnwise heatmap table")
Table 8. Columnwise heatmap table
  mpg cyl disp hp drat wt qsec vs am gear carb
Mazda RX4 21.00 6.00 160.00 110.00 3.90 2.62 16.46 0.00 1.00 4.00 4.00
Mazda RX4 Wag 21.00 6.00 160.00 110.00 3.90 2.88 17.02 0.00 1.00 4.00 4.00
Datsun 710 22.80 4.00 108.00 93.00 3.85 2.32 18.61 1.00 1.00 4.00 1.00
Hornet 4 Drive 21.40 6.00 258.00 110.00 3.08 3.21 19.44 1.00 0.00 3.00 1.00
Hornet Sportabout 18.70 8.00 360.00 175.00 3.15 3.44 17.02 0.00 0.00 3.00 2.00
Valiant 18.10 6.00 225.00 105.00 2.76 3.46 20.22 1.00 0.00 3.00 1.00

Selected Rowwise Heatmap Table

You can make selected columnwise heatmap table. You can select rows with rows argument. To make rowwise heatmap table, set the margin argument 1.

ztable(t(head(mtcars))) %>%
    makeHeatmap(palette="YlOrRd",rows=c(1,3,4),margin=1) %>%
    print(caption="Table 9. Rowwise heatmap table")
Table 9. Rowwise heatmap table
  Mazda RX4 Mazda RX4 Wag Datsun 710 Hornet 4 Drive Hornet Sportabout Valiant
mpg 21.00 21.00 22.80 21.40 18.70 18.10
cyl 6.00 6.00 4.00 6.00 8.00 6.00
disp 160.00 160.00 108.00 258.00 360.00 225.00
hp 110.00 110.00 93.00 110.00 175.00 105.00
drat 3.90 3.90 3.85 3.08 3.15 2.76
wt 2.62 2.88 2.32 3.21 3.44 3.46
qsec 16.46 17.02 18.61 19.44 17.02 20.22
vs 0.00 0.00 1.00 1.00 0.00 1.00
am 1.00 1.00 1.00 0.00 0.00 0.00
gear 4.00 4.00 4.00 3.00 3.00 3.00
carb 4.00 4.00 1.00 1.00 2.00 1.00