Uganda is traversed by the East African Rift System (EARS), which controls its topography and induces high seismicity in the southwestern and western parts of the country, around the Rwenzori Mountains and Albertine Graben. This paper explores the complexity of the geophysical, topographic and geomorphological settings of Uganda for linking the distribution and magnitude of earthquakes to the controlling factors: geomorphology, topography and geophysics. The methodological workflow for an automated plotting of the topographic, geophysical and seismic data includes the following important codes: 'gmt grdimage ug_relief.nc-Cgeo.cpt-R29/35/-1.5/4.3-JM6.5i-I+a15+ne0.75-t50-Xc-P-K > $ps' for topographic visualisation, 'gmt psxy-R-J quakes_UG.ngdc-Wfaint-i4,3,6,6s0.1-h3-Scc-Csteps.cpt-O-K >> $ps' for mapping earthquakes, 'gmt img2grd grav_27.1.img-R29/35.5/-1.5/4.3-Ggrav_UG.grd-T1-I1-E-S0.1-V' for mapping gravity. The steps of the scripting workflow using 'raster' and 'tmap' libraries of R and a variety of GMT modules includes the following most important codes: 'alt = getData("alt", country = "Uganda", path = tempdir()); slope = terrain(alt, opt = "slope"); aspect = terrain(alt, opt = "aspect"); hill = hillShade(slope, aspect, angle = 40, direction = 270)'. The study uses high-resolution spatial datasets GEBCO, EGM-2008, IRIS, gravity grids and SRTM DEM aimed to undertake thematic mapping of Uganda. Nine new maps have been generated using shell scripts of GMT and R for environmental monitoring. Depth of the earthquakes ranges from 4 to 40 Km with frequency of seismic events near Rwenzori Mountains and Albertine Graben for destructive earthquake is less than about five decades. Earthquake magnitudes varied from 3.7 Richter Magnitude Scale (Lake Edward region) to 6.2 Richter local magnitude Makerere scale (M L) (Lake Albert region). Lake Kivu region has earthquakes with magnitudes between 3.8-5.3. The region of Lake Albert had the highest magnitudes and frequency of seismic events, compared to Lakes Kivu and Edward. Earthquakes around the Lake Albert reached the highest magnitude at 6.2 M L. Earthquakes around Lake Victoria reach the maximal level of earthquake magnitude at 5.0 M l , near Lake George-5.3 M L. Earthquakes were mostly recorded in the Albertine Graben of EARS in the Albert, Edward and George lakes and occasionally in Lake Victoria.