Make a Heatmap Table using `ztable`

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = NA,
  message=FALSE
)

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

Basic Table

You can make html or LaTex table easily with ztable.

library(ztable)
library(magrittr)
options(ztable.type="html")
z=ztable(x) 
print(z,caption="Table 1. Basic Table")

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")

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") 

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 makeHeatmap() function apply the "Reds" palette from RColorBrewer package.

z %>% makeHeatmap() %>% print(caption="Table 4. Heatmap Table")

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")

Heatmap Table with user-defined palette

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

mycolor=gradientColor(low="yellow",mid="orange",high="red",n=20,plot=TRUE)
mycolor
ztable(head(mtcars[1:5])) %>% 
    makeHeatmap(mycolor=mycolor) %>%
    print(caption="Table 6. Heatmap table with user-defined palette")

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")

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")

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")


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ztable documentation built on Oct. 23, 2020, 5:58 p.m.