Scatter plot of two data frames using ggplot and add a Loess line in R

Question

I have two data frames which dimension are 24,523 × 3,468, and I want to get the scatter plot of them (data frame 1 in axis x and data frame 2 in axis 2)> then, I want to add a Loess line.

I can simply use a function plot() to get the scatter plot, but I do not know how to add a Loess line to the plot. Furthermore, I found that if the data for each axis is one vector only, instead of data frames, it can be done directly using a function called stat_smooth() in ggplot2 package.

My question is 1) how to get a scatter plot of two data frames using a function ggplot()? 2) How to add a Loess line to a scatter plot generated using two data frames?

This is what I get using

plot(as.matrix(spatial_data_glio_df_intersection_genes), as.matrix(estimated_all_gene_read_counts_spatial), xlab = "true_gene_read_counts", ylab = "estimated_gene_read_counts")

The data can be accessed using the link data.

Answer 1

Just linearize the two data frames with as.vector(). I've made a minimum reproducible example using random data. The first plot corresponds more or less to what you have currently, the second one hopefully corresponds to the desired output:

library(ggplot2)

df1 <- matrix(rnorm(1000), nrow = 100)
df2 <- matrix(rnorm(1000), nrow = 100)

plot(df1, df2, xlab = "true_gene_read_counts", ylab = "estimated_gene_read_counts")

joint_df <- data.frame(df1 = as.vector(df1), df2 = as.vector(df2))

ggplot(joint_df, aes(df1, df2)) +
    geom_point() +
    geom_smooth(method = "loess") +
    labs(x = "true_gene_read_counts", y = "estimated_gene_read_counts") +
    theme_linedraw()