CODEWITHSUNDEEP
rlinear-regressioncluster-analysisheatmappheatmap
user3351676
user3351676

Reputation: 91

R pheatmap How to plot a linear model?

I have a classical linear model y ~ x1 + x2. How can I plot a heatmap of this model? Normally I print a heatmap from data in this way:

library(pheatmap)

data <- data.frame(y=c(1,2,3), x1=c(1.5,2,2.5), x2=c(3,10,12))
pheatmap(cor(data), scale="none")

But in this case I want to see the effect of y on x1 and x2. So I need a heatmap with a covariate for y. Something like this:

pheatmap(cor(select(data,-c(y))), scale="none", covariate=y)

But i didn't find a correct syntax for y as covariate. Please help me.

Upvotes: 1

Views: 98

Answers (1)

DaveArmstrong
DaveArmstrong

Reputation: 22044

How about something like this (where y is qsec, x1 is hp and x2 is wt:

library(tidyr)
library(ggplot2)
data(mtcars)

mod <- lm(qsec ~ hp + wt, data=mtcars)

hp_s <- seq(min(mtcars$hp), max(mtcars$hp), length=25)
wt_s <- seq(min(mtcars$wt), max(mtcars$wt), length=25)

eg <- expand_grid(hp = hp_s, wt=wt_s)
eg$fit <- predict(mod, newdata=eg)

ggplot(eg, aes(x=hp, y=wt, fill=fit)) + 
  geom_tile() + 
  scale_fill_viridis_c() + 
  theme_classic()

Created on 2022-11-27 by the reprex package (v2.0.1)

Upvotes: 1

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