I want to create ggplot where X axis will include data from one column of the data frame and Y axis will include data from other column of the data frame.
This is the command:
ggplot()+
geom_point(diseases_california,mapping = aes(x=diseases_california[,6], y=diseases_california[,7]))
FJCC is right, but even with your syntax you should be getting a result, so it is very likely that there is a problem with the structure of your data set. In order to help you with that please provide a minimal REPRoducible EXample (reprex) of your issue.
For example this is a reprex with some built-in data, you could do the same but with a subset of your own data.
library(ggplot2)
diseases_california <- iris # Madeup data
ggplot() +
geom_point(diseases_california, mapping = aes(x = diseases_california[,1],
y = diseases_california[,2]))