[英]How to plot a heat map by chromosome in R
I have a data table in the following format: 我有一个以下格式的数据表:
set.seed(1)
dt <- data.table(
chromosome = c(rep(1, 100),
rep(2, 100),
rep(3, 80)),
mb_from = c(seq(1, 1000, by=10),
seq(1, 1000, by=10),
seq(1, 800, by=10)),
mb_to = c(seq(10, 1000, by=10),
seq(10, 1000, by=10),
seq(10, 800, by=10)),
score = c(sample(1:10, 100, replace = T),
sample(1:10, 100, replace = T),
sample(1:10, 80, replace = T))
)
And I am trying to plot a figure similar (but not identical) to this: 我试图绘制一个类似(但不完全相同)的数字:
I have tried using ggplot and geom_rect(), but with no luck. 我尝试过使用ggplot和geom_rect(),但没有运气。
Any help will be greatly appreciated. 任何帮助将不胜感激。
You could try the plotly
package, here's a start: 你可以尝试一下plotly
包,这是一个开始:
library(dplyr)
library(plotly)
library(RColorBrewer)
dat <- apply(dt,
1,
function(x) data.table(chromosome = x["chromosome"], mb = x["mb_from"]:x["mb_to"], score = x["score"])
) %>%
rbindlist()
plot_ly(dat, x = ~chromosome, y = ~mb, z = ~score, type = "heatmap",
colors = "RdYlBu", reversescale = T) %>%
layout(yaxis = list(range = c(1000, 0)))
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