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Heatmap in R; how to change the order of Row names

Hello, Biostars,

I am working on generation of Heatmap.

My R code used for that is:

Heatmap(heat,
        name = "Log2",
        col = color_fun,
        split = df$Family,
        cluster_rows = T,
        show_row_dend = F,
        show_row_names = F,
        row_title_side = "left",
        row_title_gp = gpar(fontsize = 12, fontface = "bold"),
        row_names_side = "left",
        row_title_rot = 0,
        width = unit(4, "cm"))

And then, I have this figure:

enter image description here

Since I run cluster_row = T function, the order of row is not from 1 to 9. How could I make it from 1 to 9 keeping clustering?

Thank you.

r complexheatmap
• 2,057 views • link
updated by Ram Ram • written by hellokwmin • hellokwmin

Hi, One reason this is happening is because of the dendogram. Disable the dendogram for the columns and then check. In most usual cases it sorts the rows order wise

• 0 views • link
written by Eshwari • Eshwari

Alternatively you could use ggplots geom_tile to make the heatmap. Then you could set facet_wrap(~Family), and change the order by setting the factor

df$Family = factor(df$Family, levels=c( ....   ))
• 0 views • link
updated by Ram Ram • written by noodlejackson • noodlejackson

1 answer

You can add cluster_row_slices = F to your code.

head(heat)
C1         C2
R1 -0.56047565 -0.6947070
R2 -0.23017749 -0.2079173
R3  1.55870831 -1.2653964
R4  0.07050839  2.1689560
R5  0.12928774  1.2079620
R6  1.71506499 -1.1231086

Heatmap(heat, name = "Log2", col = color_fun, split = df$Family,  
         cluster_rows = T, show_row_dend = F, show_row_names = F,   
         row_title_side = "left", row_title_gp = gpar(fontsize = 12, fontface = "bold"), 
         row_names_side = "left", row_title_rot = 0, width = unit(4, "cm"), cluster_row_slices = F)

OR you can do km=9 (I m seeing 9 row clusters in your figure) and modify your code like this:-

Heatmap(heat, name = "Log2", col = color_fun,  cluster_rows = T, 
                show_row_dend = F, show_row_names = F, row_title_side = "left", 
                row_title_gp = gpar(fontsize = 12, fontface = "bold"), row_names_side = "left", 
                row_title_rot = 0, width = unit(4, "cm"), km=9, cluster_row_slices = F)

enter image description here

• 0 views • link
updated by Ram Ram • written by bk11 • bk11

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