Plotting multiple line graphs in one using R

Question

I have a dataset with the number of reads for more than 3000 organisms obtained on 3 different stages of experiment. The data looks something like this:

          rain      day0      day7
 org1     923857    505062    503292
 org2     424002    198440    26314
 org3     2910      1492      535

...with 3000 more rows trailing this.

I want to plot the trend (number of reads) for each organism across different stages.. (start, day0, day7). Each organism should be represented with a different color and all should be in the same plot.

I have tried doing the same in excel but it has a limit of only 255 such lines in a single plot.

The plot I obtained in excel:

Is there a way of doing this in R? I am new to R and therefore don't know much. I think ggplot might work but I'm having hard time understanding how to use it on this data.

Any help is greatly appreciated. Thanks.

Answer 1

Here is a version using library(tidyverse)

I created a data.frame based upon the data you provided,
gather these variables to put the data into a long format,
changed the factor levels so that they align with the plot you provided,
and used ggplot to produce a figure.

data.frame(org = letters[1:3],
           rain = c(923857, 424002, 2910),
           day0 = c(505062, 198440, 1492),
           day7 = c(503292, 2614, 535)) %>% 
  gather(variable, value, -org) %>% 
  mutate(variable = factor(variable, levels = c('rain', 'day0', 'day7'))) %>% 
  ggplot(aes(variable, value, color = org, group = org)) + 
  geom_point() +
  geom_line() +
  theme(legend.position="bottom")