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rgraphtime-seriesline

Using ggplot2 (or comparable package) to plot line graph of time-series expression data

I am trying to use R to make a line graph of time-series data for a genes expression level in two replicates (Rep2 and Rep3) over the course of 12-72 hours (points every two hours). I am a beginner at R and have looked at examples of making other time-series graphs on here and am still confused. I would appreciate any help you can give!

Here is what my dataframe looks like: enter image description here

Here is what I'd like my final graph to look like: enter image description here

Solution

  • Without the data to test this, I can't know if it will work. I didn't feel like transcribing the photo of your spreadsheet. I feel like this will get you 90% of the way to the plot you show. The key is to go from wide format to long and then parse the numbers so they can be plotted.

    library(tidyverse)

df |>
  pivot_longer(cols = contains("X"), names_to = "HPS", values_to = "TPM")|>
  mutate(HPS = parse_number(HPS))|>
  ggplot(aes(HPS, TPM, color = gene_id))+
  geom_point()+
  geom_line()+
  ggtitle("Arntl")+
  scale_color_manual(values = c("blue", "orange"))+
  theme_bw()+
  theme(legend.position = "bottom",
        legend.direction = "horizontal")