I would like to visualize my data using the Heatmap
function from the ComplexHeatmap
package, which I find to be a very good combination of annotations and expression values in one image.
Unfortunately I am not sure, what I'm doing wrong here. My heatmap shows just one color.
The code to create the Heatmap is
col_fun = colorRamp2(c(-3, 0, 3), c("green", "white", "red"))
Heatmap(mat, name = "expression", km = 8, top_annotation = ha,
show_row_names = FALSE, show_column_names = FALSE, col=col_fun) +
Heatmap(expr$gene_biotype, name = "biotype", width = unit(5, "mm"),
col = circlize::rand_color(length(unique(expr$gene_biotype))) )
mat
is a matrix of RNA-Seq expression values, normalized with the DESeq2 package. It contains all significantly deregulated genes (11332 genes with padj <= 0.05).
There are strong fluctuations within the data (see the summary below)
> summary(mat)
01_Flox_S13 02_Flox_S1 03_Flox_S21 04_Flox_S17 05_Flox_S27 06_Rab7KO23_S28
Min. : 0.0 Min. : 0.0 Min. : 0.0 Min. : 0.0 Min. : 0.0 Min. : 0.0
1st Qu.: 241.4 1st Qu.: 248.3 1st Qu.: 241.2 1st Qu.: 245.9 1st Qu.: 244.5 1st Qu.: 257.7
Median : 990.6 Median : 999.9 Median : 987.7 Median : 1003.4 Median : 992.1 Median : 1031.4
Mean : 2505.1 Mean : 2502.6 Mean : 2492.8 Mean : 2515.5 Mean : 2503.8 Mean : 2558.4
3rd Qu.: 2621.8 3rd Qu.: 2653.3 3rd Qu.: 2612.4 3rd Qu.: 2648.7 3rd Qu.: 2637.9 3rd Qu.: 2609.6
Max. :274498.5 Max. :272329.5 Max. :275464.8 Max. :265434.6 Max. :267117.7 Max. :275797.9
07_Rab7KO23_S24 08_Rab7KO23_S23 09_Rab7KO23_S29 10_Rab7KO23_S8 11_Rab7KO25_S5 12_Rab7KO25_S19
Min. : 0.0 Min. : 0.0 Min. : 0.0 Min. : 0.0 Min. : 0.0 Min. : 0.0
1st Qu.: 256.7 1st Qu.: 254.5 1st Qu.: 256.3 1st Qu.: 252.8 1st Qu.: 260.9 1st Qu.: 255.5
Median : 1028.7 Median : 1021.7 Median : 1017.2 Median : 1026.0 Median : 1026.5 Median : 1023.3
Mean : 2502.9 Mean : 2507.6 Mean : 2498.0 Mean : 2514.1 Mean : 2540.8 Mean : 2516.9
3rd Qu.: 2602.2 3rd Qu.: 2591.6 3rd Qu.: 2584.8 3rd Qu.: 2595.6 3rd Qu.: 2576.9 3rd Qu.: 2608.9
Max. :256343.7 Max. :259078.5 Max. :250331.2 Max. :267339.0 Max. :310160.6 Max. :301711.7
13_Rab7KO25_S16 14_Rab7KO25_S15 15_Rab7KO25_S2
Min. : 0.0 Min. : 0.0 Min. : 0.0
1st Qu.: 257.8 1st Qu.: 257.2 1st Qu.: 256.7
Median : 1027.5 Median : 1021.9 Median : 1028.9
Mean : 2519.0 Mean : 2520.9 Mean : 2513.1
3rd Qu.: 2599.7 3rd Qu.: 2604.9 3rd Qu.: 2590.6
Max. :303185.3 Max. :299469.0 Max. :305042.9
The results of this command can be seen to the left in the image below, while the results of my heatmap.2
command is to the right (where the colors are much more distinguish between up- and down-regulated genes).
Do I somehow need to scale the data before plotting it?
Thanks for any advice.
thanks, I figure this was my problem.