It is a major pain. Try "R". It is nearly entirely engineered toward proper handling of data. Exploratory Data Analysis (EDA) is so fundamental to the stats folks who make R that NIST dedicated a good chunk of their manual to it. (http://www.itl.nist.gov/div898/handbook/eda/eda.htm)
Use whatever's most convenient and good enough, sometimes that's gnuplot, sometimes that's matplotlib, sometimes that's ggplot, sometimes that's some javascript thing.
It is a major pain. Try "R". It is nearly entirely engineered toward proper handling of data. Exploratory Data Analysis (EDA) is so fundamental to the stats folks who make R that NIST dedicated a good chunk of their manual to it. (http://www.itl.nist.gov/div898/handbook/eda/eda.htm)
Rstudio is nice. ggplot2 is excellent.