Annotation of Complex Heatmap

Question

[abiuma]

Hi,

I would like add this metadata to my heatmap. I have a couple of issues 1) I am not able to assign the colours I want 2) How do I get all the celltypes under one legend. Currently with this command I get 2 different legends for each cell type. Could some one help me.

This is my Metadata:

IDs  celltype1  celltype2
ID1     Cells_1    
ID2     Cells_1    Cells_2
ID3     Cells_1    Cells_2
ID4                     Cells_2
ID5     Cells_1    
ID6     Cells_1    Cells_2

This is my code

ann_P_Merge <- data.frame(Metadata$celltype1, Metadata$celltype2 )

colnames(ann_P_Merge) <- c('celltype1', 'celltype2 ')

type_colors <- list('Celltypes' = c('celltype1' = 'royalblue', 'celltype2 ' = 'magenta'))

colAnn_P_Merge <- HeatmapAnnotation(
  df = ann_P_Merge,
  which = 'col',
  col = type_colors ,
  annotation_width = unit(c(1, 4), 'cm'),
  gap = unit(1, 'mm'), gp = gpar(col = "black", fontsize = 25)
)

ht1 = Heatmap((t(df4)), name = "Test", col = col_fun, rect_gp = gpar(col = "black", lwd = 0.5), cluster_columns = FALSE, cluster_rows = TRUE,
              top_annotation= colAnn_P_Merge, row_names_gp = gpar(fontsize = 10, "fontface" = "bold"), 
              column_names_gp = gpar(fontsize = 10))

[jv]

How do I get all the celltypes under one legend.

You have two columns of metadata which is why you get two legends.

To get a single legend you would need to combine the labels across celltype1 and celltype2, e.g.,

IDs	celltype1	celltype2	Single Label
ID1	Cells_1		Cells_1
ID2	Cells_1	Cells_2	Cells_1&2
ID3	Cells_1	Cells_2	Cells_1&2
ID4		Cells_2	Cells_2

[jv]

Alternatively, have you looked at options for adding a custom legend? See https://jokergoo.github.io/ComplexHeatmap-reference/book/legends.html#add-customized-legends

[abiuma]

Thanks..I got it to work now.

[abiuma]

Thanks! Then how would the heatmap look? The compleas heatmap tutorial only shows 2 different bars that we can give for the metadata. It does not show we can do 2 different metadat in one bar. If I am to make a bar with the Single Label column, would the complex heatmap divide the colored boxes and make into 2?..

This is the example complex heatmap provides. Here it shows 2 annotations foo and bar in different rows.

[jv]

you can add as many annotations as you want, there's no limit to just 2.