ggplot2 problem many variables

Question

[dimitrischat]

First of, sorry if i dont explain this the right way. I am R-studio noobie and i am trying to plot this data shown below, but no success. I want for example in x-axis to show the hits column, the y-axis to show the clusters column and to seperate these via color from species column. For example i also included what i wrote in R studio but i am guessing its totally wrong. Thanks in advance

ggplot(mydata, aes(x=hits, y = clusters,group = 1, colour = species)) +
  geom_point() +
  xlim(1000,100000) +
  geom_line()


    clusters    hits    species
2 or more   100000  homo sapiens
3 or more   29411   homo sapiens
4 or more   14998   homo sapiens
5 or more   8655    homo sapiens
2 or more   250000  mus musculus
3 or more   100000  mus musculus
4 or more   56088   mus musculus
5 or more   32181   mus musculus
2 or more   100000  chimp
3 or more   30783   chimp
4 or more   14760   chimp
5 or more   8063    chimp
2 or more   2149    drosophila
3 or more   173 drosophila
4 or more   39  drosophila
5 or more   23  drosophila
2 or more   26402   Zebrafish
3 or more   7462    Zebrafish
4 or more   3557    Zebrafish
5 or more   2122    Zebrafish
2 or more   2757    C elegans
3 or more   409 C elegans
4 or more   115 C elegans
5 or more   56  C elegans
2 or more   243 Cerevisiae
3 or more   29  Cerevisiae
4 or more   8   Cerevisiae
5 or more   4   Cerevisiae
2 or more   25066   Zea mays
3 or more   2921    Zea mays
4 or more   940 Zea mays
5 or more   581 Zea mays
2 or more   3551    Arabidopsis thaliana
3 or more   482 Arabidopsis thaliana
4 or more   122 Arabidopsis thaliana
5 or more   43  Arabidopsis thaliana

[Asaf]

I guess you'll have to remove the or more from clusters

Answer 1

[Ram]

I don't understand what you're trying to accomplish with the geom_line(), but your code works fine for me:

bdat <- read.table(sep="\t", quote="", stringsAsFactors = FALSE, header = TRUE, text = "clusters    hits    species
2 or more   100000  homo sapiens
3 or more   29411   homo sapiens
4 or more   14998   homo sapiens
5 or more   8655    homo sapiens
2 or more   250000  mus musculus
3 or more   100000  mus musculus
4 or more   56088   mus musculus
5 or more   32181   mus musculus
2 or more   100000  chimp
3 or more   30783   chimp
4 or more   14760   chimp
5 or more   8063    chimp
2 or more   2149    drosophila
3 or more   173 drosophila
4 or more   39  drosophila
5 or more   23  drosophila
2 or more   26402   Zebrafish
3 or more   7462    Zebrafish
4 or more   3557    Zebrafish
5 or more   2122    Zebrafish
2 or more   2757    C elegans
3 or more   409 C elegans
4 or more   115 C elegans
5 or more   56  C elegans
2 or more   243 Cerevisiae
3 or more   29  Cerevisiae
4 or more   8   Cerevisiae
5 or more   4   Cerevisiae
2 or more   25066   Zea mays
3 or more   2921    Zea mays
4 or more   940 Zea mays
5 or more   581 Zea mays
2 or more   3551    Arabidopsis thaliana
3 or more   482 Arabidopsis thaliana
4 or more   122 Arabidopsis thaliana
5 or more   43  Arabidopsis thaliana
")

ggplot(bdat, aes(x=hits, y = clusters,group = 1, colour = species)) + geom_point() + xlim(1000, 100000)
Warning message:
Removed 16 rows containing missing values (geom_point).

## Remove all data points <1000 and >100000 as they're not being plotted anyway
ggplot(bdat[bdat$hits>=1000 & bdat$hits<=100000,], aes(x=hits, y = clusters,group = 1, colour = species)) + geom_point() + xlim(1000, 100000) + geom_line()

[dimitrischat]

thanks a lot for your help! It does work, i tried it with xlim(1,250000) if you can also try it, i dont understand why the line from 250.000 to 100.000 which is mus musculus is green but the color for mus musculus on the color legened on the right is blue (?)

https://ibb.co/0jV7fpF