CompleX heat Map

Question

[Sidra]

I have this R script for Complex Heat map, code is ok but the problem is the legend size. i am unable to adjust the legend size on the right side of the diagram.

## Install Packages

#install.packages("dplyr")
#install.packages("tidyr")
#install.packages("plyr")
#install.packages("reshape2")
#install.packages("ComplexHeatmap")
#install.packages("ggpubr")
#install.packages("circlize")
#install.packages("RColorBrewer")
#install.packages("scales")
#install.packages("stringdist")
#install.packages("corrplot")
#install.packages("heatmaply")

## Call Libraries
library(dplyr)
library(tidyr)
library(plyr)
library(reshape2)
library(ComplexHeatmap)
library(ggpubr)
library(circlize)
library(RColorBrewer)
library(scales)
library(stringdist)
library(corrplot)
library(heatmaply)


## Calling CSV file of interest and data formating

mydf_orig <- read.csv("plamid_data.csv", header = FALSE)
mydf <- mydf_orig  %>%  mutate_all(trimws)
mydf[,1]
mydf[2,]

rownames(mydf)<-mydf[,1]
colnames(mydf)<-mydf[2,]

mydf<-mydf[-c(1,2),]
mydf2 <- mydf[order(mydf[,2]),]
mydf<-mydf2[,-c(1,2)]
class(mydf)

mat<- as.matrix(mydf)
head(mat)
#write.csv(mat, file="matrix.csv")

## Starting the data manipulation for complex heatmap

# Annotation for Classes.
Antibiotics <- t(mydf_orig[1,-c(1,2)])
Antibiotics

Antibiotics_unique <- t(unique(Antibiotics))
Antibiotics_unique

colourCount_Antibiotics = length(Antibiotics_unique)
colourCount_Antibiotics

getPalette = colorRampPalette(brewer.pal(9, "Set1"))

Antibiotics_colors<- getPalette(colourCount_Antibiotics)
Antibiotics_colors

show_col(Antibiotics_colors)

list_antibiotics_colors <- setNames(Antibiotics_colors, Antibiotics_unique)
list_antibiotics_colors

h_antib = HeatmapAnnotation(Antibiotics = Antibiotics,
                            col = list(Antibiotics= list_antibiotics_colors),
                            gp = gpar( col = rep(2:3, each = 2)),

                            border = TRUE)

plot(h_antib)

## Annotation for Locations.

Cities <- (mydf2[,2])
Cities

Cities_unique <- t(unique(Cities))
Cities_unique

colourCount_Cities = length(Cities_unique)
colourCount_Cities

getPalette2 = colorRampPalette(brewer.pal(9, "Set3"))
colors_Cities<- getPalette2(colourCount_Cities)
colors_Cities

show_col(colors_Cities)

col2_cities <- setNames(colors_Cities, Cities_unique)

h_cities= rowAnnotation(Cities = Cities,
                        col = list(Cities= col2_cities),
                        gp = gpar(fontsize = 3),
                        border = TRUE)

plot(h_cities)

## Generation of colors for conditions.

condition_colors <- c("#36D3C4","#D33636")

condition_colors_list = structure(condition_colors, names = c("1","0"))
condition_colors_list
show_col(condition_colors_list)

haha <- setNames(condition_colors, c("1","0"))
haha
show_col(haha)

## Generation of dendogram for character data.

# For calculating distances using stringdist package
dist_letters = function(x, y) {
  x = strtoi(charToRaw(paste(x, collapse = "")), base = 16)
  y = strtoi(charToRaw(paste(y, collapse = "")), base = 16)
  sqrt(sum((x - y)^2))
}

fA =c("A","A","B")
fB=c("A","A","B")
dist_letters(fA,fB)

fA=c("A","A","A")
fB =c("Z","Z","Z")
dist_letters(fA,fB)

#between 1st and 2nd row
dist_letters(mat[1,],mat[2,])

#between 1st and 2nd column
dist_letters(mat[,1],mat[,2])

## Calculation of frequencies of R, I and S.

table(mydf[,1],useNA = "ifany")
lapply(mydf, table)

factors <- sort(unique(unlist(mydf)))
factors

total_IRS<- as.data.frame(do.call(rbind, lapply(mydf, function(x) table(factor(x, levels=factors)))))
total_IRS

total <- tibble::rownames_to_column(total_IRS, "Antibiotic")
total

total_t<- t(total)
total_t

colnames(total_t)<-total_t[1,]
total_t <- total_t[-1,]
total_t

class(total_t) <- "numeric"

## Annotation of Frequency Plot for Heatmap

h_frequencies = HeatmapAnnotation(Frequencies=anno_barplot(t(total_t),
                                                           gp=gpar(fill = condition_colors, 
                                                                   col = condition_colors)))
plot(h_frequencies)

## Generation of Heatmap

Heatmap(mat, name = "Condition",
        border_gp = gpar(col = "black", lty = 2),
        clustering_method_rows = "single",
        column_title = "Heatmap",
        column_title_gp = gpar(fontsize =5, fontface = "bold"),
        col = condition_colors_list,
        row_title = "Isolates",
        bottom_annotation = h_antib ,
        top_annotation = h_frequencies,
        right_annotation =h_cities,
        column_km = 1,
        row_names_side = "left",
        row_names_gp = gpar(fontsize = 5),
        show_row_names = FALSE,
        column_names_rot = 1,
        column_names_gp = gpar(fontsize = 5),
        heatmap_height = unit(0.25, "mm")*nrow(mat),
        #clustering_distance_rows = dist_letters,
        clustering_distance_columns = dist_letters,
        row_dend_reorder = FALSE,
        column_dend_reorder = FALSE,
        heatmap_width = unit(1.5, "mm")*ncol(mat),
)

Answer 1

[bkleiboeker]

You can adjust legend width, legend height, and legend fontsize with the following 3 arguments to heatmap_legend_param

h <- Heatmap(...,
         heatmap_legend_param = list(legend_width = unit(7, "cm"),
                                     legend_height = unit(4, "cm"),
                                     labels_gp = gpar(fontsize = 2)))

And can adjust legend location with:

draw(h, heatmap_legend_side = "bottom")

This package always works better for me when I make a ComplexHeatmap object (here, h) and then call it in a separate draw() function.