Entering edit mode
4.0 years ago
mohammedtoufiq91
▴
260
Hi,
I have a question about customizing the fold change legend values applied on a data matrix in R. I am plotting the heatmap on my data matrix using the library(ComplexHeatmap)
and library(circlize)
. However, when I try to input values in col_fun
in the range of (-2,0,2) or even (-2,0,5). It always displays (-4,0,4) in the legend bar. Please assist me in customizing fold change legend values. Here is my code.
class(my_matrix)
[1] "matrix" "array"
str(my_matrix)
num [1:12, 1:10] 0.436 -0.143 -0.097 0 0.168 ...
- attr(*, "dimnames")=List of 2
..$ : chr [1:12] "Gene A" "Gene B" "Gene C" "Gene D" ..
col_fun = circlize::colorRamp2(c(-2,0,2), c("blue", "white", "red"))
pdf("Heatmap.pdf",height = 5, width = 7)
ht=Heatmap(my_matrix,
name = "Fold Change Values",
na_col = "grey",
cluster_rows = F,
cluster_columns = F,
#height = unit(4, "mm")*nrow(df_plot),
#width = unit(4, "mm")*ncol(df_plot),
rect_gp = gpar(type = "none"),
top_annotation = column_ha,
#name = "% Response",
row_names_max_width = unit(10,"in"),
row_title_gp = gpar(fontsize = 0.1),
column_names_gp = gpar(fontsize = 12),
row_names_gp = gpar(fontsize = 13),
cell_fun = function(j, i, x, y, width, height, fill) {
grid.circle(x = x, y = y, r = unit(1.85, "mm") ,gp = gpar(fill = col_fun(my_matrix[i, j]), col = NA))
}
)
draw(ht,heatmap_legend_side = "left", annotation_legend_side = "right", padding = unit(c(2, 20, 2, 2), "mm"))
dev.off()
Thank you,
Toufiq
You are overwriting the custom values you set on top of the script with
col_fun(my_matrix[i, j])
are you aware of that?Hi @ATpoint, thank you for your prompt reply.
I tried running this code, however,
It's
col = circlize::colorRamp2(c(-2,0,2), c("blue", "white", "red"))
notcol_fun
. Use?Heatmap
to check parameters correct name.I wanted to input (-3,0,6), now I can see in the legend. Thank you so much.