Complexheatmap annotation legend

Question

[Prakash]

Hi all,

could somebody help me in complexheatmap annotation legend.

hmap1 hmap2 hmap1+hmap2

Here if I merge hmap1 and hmap2, the legend for hmap2 goes missing. I am using complexheatmap version 1.99.5.

oxp_map1 file1

oxp_map2 file2

anno <- as.data.frame(colnames(oxp_exp_X_scaled[,1:4]))
colnames(anno) <- "Sample"
anno$Vector <- c("Empty","KD","Empty","KD")
anno$Time <- c("0h","0h","6h","6h")
ha = HeatmapAnnotation(df=anno[,c(2:3)], 
                   col = list(Vector = c("Empty"="red","KD"="grey"),
                              Time = c("0h"="dimgray","6h"="brown")),
                   annotation_height = unit(c(0.5, 0.5), "cm"),
                   show_annotation_name = TRUE,
                   annotation_name_offset = unit(2, "mm"),
                   annotation_name_rot = c(0, 0))

 oxp_map1 <- Heatmap(oxp_exp_X_scaled[,1:4],km = 1,
                name="Z-score",
                col= colorRamp2(c(-2,-1,0,1,2),c("blue","skyblue","white","lightcoral","red")),
                heatmap_legend_param=list(at=c(-2,-1,0,1,2),color_bar="continuous", 
                                          legend_direction="horizontal", legend_width=unit(5,"cm"),
                                          title_position="topcenter", title_gp=gpar(fontsize=10, fontface="bold")),

                #Split heatmap rows by gene family
                split = oxp_exp_X_scaled[,5],
                border = TRUE,

                cluster_rows=TRUE,
                show_row_dend=TRUE,
                row_title_side="left",
                row_title_gp=gpar(fontsize=8),
                show_row_names=TRUE,
                row_names_side="right",

                #Column annotation configuratiions
                cluster_columns=FALSE,
                show_column_dend=TRUE,
                column_title="X",
                column_title_side="top",
                column_title_gp=gpar(fontsize=10, fontface="bold"),
                show_column_names=FALSE,

                #Dendrogram configurations: columns
                clustering_distance_columns="euclidean",
                clustering_method_columns="complete",
                column_dend_height=unit(10,"mm"),

                #Dendrogram configurations: rows
                clustering_distance_rows="euclidean",
                clustering_method_rows="complete",
                row_dend_width=unit(10,"mm"),
                top_annotation = ha,
                show_heatmap_legend = TRUE)
        #################################################
       # Row annotation

       RowAnn <- data.frame(paste0("Complex",oxp_exp_Y_scaled[,7]))
       colnames(RowAnn) <- c("Complex")
        RowAnn <- HeatmapAnnotation(df=RowAnn, which="row")

        # Top annotation
        anno <- as.data.frame(colnames(oxp_exp_Y_scaled[,1:6]))
        colnames(anno) <- "Sample"
        anno$Vector <- c("Empty","KD","Empty","KD","Empty","KD")
        anno$Time <- c("0h","0h","2h","2h","6h","6h")
        ha2 = HeatmapAnnotation(df=anno[,c(2:3)],
                    col = list(Vector = c("Empty"="red","KD"="blue"),
                               Time = c("0h"="dimgray","2h"="gray","6h"="brown")),
                    annotation_height = unit(c(0.5, 0.5), "cm"),
                    show_annotation_name = TRUE,
                    annotation_name_offset = unit(2, "mm"),
                    annotation_name_rot = c(0, 0))

       oxp_map2 <- Heatmap(oxp_exp_Y_scaled[,1:6],km = 1,
                name="Z-score",
                col= colorRamp2(c(-2,-1,0,1,2),c("blue","skyblue","white","lightcoral","red")),
                heatmap_legend_param=list(at=c(-2,-1,0,1,2),color_bar="continuous", 
                                          legend_direction="horizontal", legend_width=unit(5,"cm"),
                                          title_position="topcenter", title_gp=gpar(fontsize=10, fontface="bold")),

                #Split heatmap rows 
                split = oxp_exp_Y_scaled[,7],
                border = TRUE,

                #Row annotation configurations
                cluster_rows=TRUE,
                show_row_dend=TRUE,
                roww_title_side="left",
                row_title_gp=gpar(fontsize=8),
                show_row_names=TRUE,
                row_names_side="right",


                #Column annotation configuratiions
                cluster_columns=FALSE,
                show_column_dend=TRUE,
                column_title="Y",
                column_title_side="top",
                column_title_gp=gpar(fontsize=10, fontface="bold"),

                column_names_gp = gpar(fontsize = 20, fontface="bold"),
                show_column_names=FALSE,

                #Dendrogram configurations: columns
                clustering_distance_columns="euclidean",
                clustering_method_columns="complete",
                column_dend_height=unit(10,"mm"),

                #Dendrogram configurations: rows
                clustering_distance_rows="euclidean",
                clustering_method_rows="complete",
                row_dend_width=unit(10,"mm"),
                top_annotation = ha2)

           draw(oxp_map1+oxp_map2+RowAnn ,heatmap_legend_side="top")

Answer 1

[Kevin Blighe]

Hey, please always show the code that you have used for this. If possible, provide data that allows for a reproducible example.

[Prakash]

Hi Kevin, I have updated the post with code and file Thanks

[Kevin Blighe]

I see. Good work on the code so far.

You may have more success by plotting them via pushViewport():

pushViewport(viewport(layout=grid.layout(nr=1, nc=2)))

  pushViewport(viewport(layout.pos.row=1, layout.pos.col=1))
    draw(oxp_map1 + RowAnn, heatmap_legend_side="top", newpage = FALSE)
  popViewport()

  pushViewport(viewport(layout.pos.row=1, layout.pos.col=2))
    draw(oxp_map2 + RowAnn, heatmap_legend_side="top", newpage = FALSE)
  popViewport()

popViewport()

Please take a look at the example, here: https://support.bioconductor.org/p/87318/#87414 (the answer given in that thread is the author of ComplexHeatmap)

[Prakash]

It did work but in different way since pushViewport will only help in plotting multiple plot, but actually my concern was why the legend goes missing when i merge the plot. anyway for time being i have addressed my issue.

Thanks a lot Kevin , I really appreciate your help !