I'm trying to plot the expression of a group of genes over time. My starting dataframe is in TPM like below.
V1 MEF DAY3 DAY6 DAY9 DAY12 IPSC Arhgef12 48.9061752 76.001558 64.294236 61.0208545 66.4678191 25.11639309 Arnt2 8.6570850 11.341789 22.613930 35.2099605 36.0336247 1.30568627 Atf3 12.3444246 35.844574 17.887655 35.5792577 141.7997036 7.67626153 Bach2 2.1672173 8.311551 12.918229 14.2654167 17.2227704 0.84742111 Bbx 33.7248954 70.522302 59.295483 49.3389741 46.8598894 39.80204016
I tried doing K-Means clustering which yielded a graph with many lines, which is close to what I want.
But I'm really only interested in the average expression of this one group (not sure which method I should use to capture the trend). I tried doing a box plot instead, but this is the median, rather than the average. Ideally, I'd like to have the boxplots with centers on the averages, with each center connected by a line (like in red). And if the boxplots could be smaller that would be better.