It is customary for the independent variable to the the column variable, and for percentages to be in the direction of the causal variable. Thus in a table of gender by vote, gender would be the column variable and percentages would add to 100% in the columns. This is because you want to compare candidate percentages for men versus candidate percentages for women. Of course this all depends on the research purpose, and it is possible the researcher really does want row percentages in order to compare gender percentages across candidates. In this example, column percentages address the research question, "Are vote choices different for men compared to women?" Row percentages would address the question, "Is gender support different for Candidate A versus Candidate B versus Candidate C?"
In general, given the research question, "Is the set of percentages of various categories of y the same or different within each category of x?", you want x to be the column variable and you want column percentages.