我正在使用ComplexHeatmap来绘制数据,但是,每当我开始划分矩阵以便更容易读取时,我的行/列的顺序似乎被洗牌。
我想知道是否我没有正确指定使用什么顺序,而不是这是一个直接与ComplexHeatmap
用法相关的问题。例如,以下是否有问题:
Heatmap( as.matrix(MyData), name = "q",
column_names_rot = 0,
col = my_palette,
# ! ---> This should set the row order!!
row_order = order(rownames(as.matrix(MyData))),
# ! ---> This should set the column order!!
column_order = order(colnames(as.matrix(MyData))),
row_split = rep(c("A", "B","C", "D"), 6),
column_split = rep(c("A", "B","C", "D"), 6),
cluster_row_slices = FALSE,
cluster_column_slices =FALSE,
heatmap_legend_param = list(
title = "Legend",
col = my_palette,
at = (c(0.05,0.03,0.01,0.000001)),
legend_height = unit(6, "cm")),
)
以下参数是此问题的关键:
# ! ---> This should set the row order!!
row_order = order(rownames(as.matrix(MyData))),
# ! ---> This should set the column order!!
column_order = order(colnames(as.matrix(MyData))),
当我创建此Heatmap时,行和列不按顺序排列。例如
现在当我删除row_split
和column_split
命令时,我没有必要设置row_order
和columns_order
命令,它看起来像这样:
我后来发现,当我使用row_order
和column_order
而没有分裂时,它实际上仍然会改变我的命令?
显然,我甚至无法按照命令保留原始顺序。我想知道是否有人可以提供这方面的见解。
这是一个示例矩阵,可以从他们的supporting documents(他们覆盖row_order
,但我必须忽略的东西)。您可能希望避免重新调整名称,但我很担心修改它,因为我甚至不能自己使用这些命令。
library(devtools)
install_github("jokergoo/ComplexHeatmap", force = TRUE)
library(ComplexHeatmap)
set.seed(123)
nr1 = 4; nr2 = 8; nr3 = 6; nr = nr1 + nr2 + nr3
nc1 = 6; nc2 = 8; nc3 = 10; nc = nc1 + nc2 + nc3
mat = cbind(rbind(matrix(rnorm(nr1*nc1, mean = 1, sd = 0.5), nr = nr1),
matrix(rnorm(nr2*nc1, mean = 0, sd = 0.5), nr = nr2),
matrix(rnorm(nr3*nc1, mean = 0, sd = 0.5), nr = nr3)),
rbind(matrix(rnorm(nr1*nc2, mean = 0, sd = 0.5), nr = nr1),
matrix(rnorm(nr2*nc2, mean = 1, sd = 0.5), nr = nr2),
matrix(rnorm(nr3*nc2, mean = 0, sd = 0.5), nr = nr3)),
rbind(matrix(rnorm(nr1*nc3, mean = 0.5, sd = 0.5), nr = nr1),
matrix(rnorm(nr2*nc3, mean = 0.5, sd = 0.5), nr = nr2),
matrix(rnorm(nr3*nc3, mean = 1, sd = 0.5), nr = nr3))
)
mat = mat[sample(nr, nr), sample(nc, nc)] # random shuffle rows and columns
rownames(mat) = paste0("row", seq_len(nr))
colnames(mat) = paste0("column", seq_len(nc))
Heatmap(mat)
以下是我一直在尝试的一些例子:
#row_order = sort(rownames(as.matrix(MyData))),
#row_order = rownames((MyData)),
#row_order = sort(rownames(MyData)),
#row_order = order((gsub("row", "", rownames(MyData)))),
#row_order = order(colnames(as.matrix(MyData))),
#column_order = order(rownames(as.matrix(MyData))),
#column_order = colnames(MyData),
#row_order = order(rownames(MyData)),
#column_order = order(as.matrix(MyData)),
#row_order = order(rownames(MyData)),
#column_order = order(colnames(MyData)),
#row_order = sort(c("C1", "C2", "C3", "C4", "C5", "C6", "C1", "C2", "C3", "C4", "C5", "C6", "C1", "C2", "C3", "C4", "C5", "C6", "C1", "C2", "C3", "C4", "C5", "C6")),
#olumn_order = sort(c("C1", "C2", "C3", "C4", "C5", "C6", "C1", "C2", "C3", "C4", "C5", "C6", "C1", "C2", "C3", "C4", "C5", "C6", "C1", "C2", "C3", "C4", "C5", "C6")),
#column_order = order(colnames(MyData)),
#column_order = sort(as.numeric(as.matrix(MyData))),
#column_order = order(colnames(MyData)),
#row_order = (MyData),
#column_order = sort(colnames(as.matrix(MyData))),
#row_order = rownames(MyData),
#row_order = sort(gsub("row", "", rownames(MyData))),
#row_order = order(colnames(as.matrix(MyData))),
#column_order = sort(colnames(as.matrix(MyData))),
#row_order = order(as.numeric(gsub("row", "", rownames(as.matrix(MyData))))),
#column_order = order(as.numeric(gsub("column", "", colnames(as.matrix(MyData))))),
#row_order = order(rownames(as.matrix(MyData))),
#column_order = order(colnames(as.matrix(MyData))),
#row_order = order(rownames(as.matrix(MyData))),
#column_order = order(colnames(as.matrix(MyData))),
我认为问题在于如何正确设置拆分热图的变量。
Heatmap( (MyData), name = "namehere",
column_names_rot = 0,
col = my_palette,
cluster_rows = FALSE,
cluster_columns = FALSE,
row_split = rep(1:4, each = 6),
column_split = rep(1:4, each = 6),
heatmap_legend_param = list(
title = "Legend",
col = my_palette,
at = (c(0.05,0.03,0.01,0.000001)),
legend_height = unit(6, "cm")),
border = TRUE
)