ComplexHeatmap: change the names of a HeatmapAnnotation object
1
0
Entering edit mode
@danielcarbajo-12758
Last seen 4 weeks ago
Singapore

I am doing a ComplexHeatmap as per normal, the only difference now is that I have it inside a function that takes as input the variable name that I want to study (in the MWE below: Species).

See the my_var variable in the MWE. Literally the only thing I want to do, is to be able to assign this variable as name to the HeatmapAnnotation object (that defines the column annotations).

I cannot do the following since the name of the variable (in this case Species) is stored in my_var:

column_ha <- ComplexHeatmap::HeatmapAnnotation(
  Species = meta_df$Species,
  col = list(Species = col_vector))

Instead, what I try to do is to use a placeholder name, and then try to change column_ha name with my_var, like this:

col_list <- list(VAR = col_vector)
names(col_list) <- my_var
column_ha <- ComplexHeatmap::HeatmapAnnotation(
  VAR = meta_df[,my_var],
  col = col_list)
names(column_ha) <- my_var

This does nothing... I can see VAR in the heatmap and the colors for the Species are all messed up...

This is my MWE:

data(iris)
my_var <- 'Species'
iris_sub <- rbind(iris[iris[,my_var]=='setosa',][1:5,],
                  iris[iris[,my_var]=='versicolor',][1:5,],
                  iris[iris[,my_var]=='virginica',][1:5,])
heat_mat <- t(as.matrix(iris_sub[,-ncol(iris_sub)]))
#
meta_df <- data.frame(ID=paste0("id",rownames(iris_sub)), VAR=iris_sub[,ncol(iris_sub)])
names(meta_df)[2] <- my_var
colnames(heat_mat) <- meta_df$ID
#
palette1 <- RColorBrewer::brewer.pal(n=9, name="RdYlGn")
col_vector <- RColorBrewer::brewer.pal(3, 'Set1')
col_vector <- stats::setNames(col_vector, levels(meta_df[,my_var]))
#
col_list <- list(VAR = col_vector)
names(col_list) <- my_var
column_ha <- ComplexHeatmap::HeatmapAnnotation(
  VAR = meta_df[,my_var],
  col = col_list)
names(column_ha) <- my_var
#
complex_heat <- ComplexHeatmap::Heatmap(heat_mat, name = "value", cluster_columns = FALSE,
                                        col = palette1,
                                        top_annotation = column_ha,
                                        border = TRUE)
grDevices::png(filename="test.png", height=400, width=600)
ComplexHeatmap::draw(complex_heat)
grDevices::dev.off()

Which produces the following heatmap:

test1

... which is all wrong. See that the placeholder name VAR is still there, and the Species colors in the column annotation on top are all wrong (not col_vector which should be Set1 red, blue, green).

So the question is simple: How to assign new names to a HeatmapAnnotation object?

Please note that if I don't have the name Species stored in the my_var variable, it works well, so I don't see the problems in my code... any help is appreciated.

See this MWE for how the final heatmap should look like (here it works cause I don't have the name Species stored in the my_var variable):

data(iris)
iris_sub <- rbind(iris[iris[,'Species']=='setosa',][1:5,],
                  iris[iris[,'Species']=='versicolor',][1:5,],
                  iris[iris[,'Species']=='virginica',][1:5,])
heat_mat <- t(as.matrix(iris_sub[,-ncol(iris_sub)]))
#
meta_df <- data.frame(ID=paste0("id",rownames(iris_sub)), Species=iris_sub[,ncol(iris_sub)])
colnames(heat_mat) <- meta_df$ID
#
palette1 <- RColorBrewer::brewer.pal(n=9, name="RdYlGn")
col_vector <- RColorBrewer::brewer.pal(3, 'Set1')
col_vector <- stats::setNames(col_vector, levels(meta_df$Species))
#
column_ha <- ComplexHeatmap::HeatmapAnnotation(
  Species = meta_df$Species,
  col = list(Species = col_vector))
#
complex_heat <- ComplexHeatmap::Heatmap(heat_mat, name = "value", cluster_columns = FALSE,
                                        col = palette1,
                                        top_annotation = column_ha,
                                        border = TRUE)
grDevices::png(filename="test.png", height=400, width=600)
ComplexHeatmap::draw(complex_heat)
grDevices::dev.off()

This produces the following correct heatmap that I want to reproduce when I have the name Species stored in the my_var variable:

test2

Thanks for the help!

ComplexHeatmap • 201 views
ADD COMMENT
2
Entering edit mode
nhaus ▴ 40
@789c70a6
Last seen 2 days ago
Switzerland

You were very close. You can pass a dataframe to HeatmapAnnotation, then it should work:

library(ComplexHeatmap)
data(iris)
my_var <- 'Species'
iris_sub <- rbind(iris[iris[,my_var]=='setosa',][1:5,],
                  iris[iris[,my_var]=='versicolor',][1:5,],
                  iris[iris[,my_var]=='virginica',][1:5,])
heat_mat <- t(as.matrix(iris_sub[,-ncol(iris_sub)]))
#
meta_df <- data.frame(ID=paste0("id",rownames(iris_sub)), VAR=iris_sub[,ncol(iris_sub)])
names(meta_df)[2] <- my_var
colnames(heat_mat) <- meta_df$ID
#
palette1 <- RColorBrewer::brewer.pal(n=9, name="RdYlGn")
col_vector <- RColorBrewer::brewer.pal(3, 'Set1')
col_vector <- stats::setNames(col_vector, levels(meta_df[,my_var]))
#
col_list <- list(VAR = col_vector)
names(col_list) <- my_var
column_ha_df <- data.frame("place_holder" = meta_df[,my_var])
colnames(column_ha_df) <- my_var
column_ha <- ComplexHeatmap::HeatmapAnnotation(
  df = column_ha_df,
  col = col_list
)

complex_heat <- ComplexHeatmap::Heatmap(heat_mat, name = "value", cluster_columns = FALSE,
                                        col = palette1,
                                        top_annotation = column_ha,
                                        border = TRUE)

draw(complex_heat)
ADD COMMENT
0
Entering edit mode

Thanks again! I also posted my follow-up question here, if you can have a look! ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns Thanks again!

ADD REPLY

Login before adding your answer.

Traffic: 531 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6