This paper describes a scripting cartographic techniques that automatically generate maps from open source spatial data using syntax of General Mapping Tools (GMT) and R. A case study present mapping East Africa with a focus on Malawi. In this study, two different approaches of scripting cartography using R programming language and GMT were studied for geophysical analysis aimed to visualize a series of eight new maps in Malawi: topography based on the GEBCO data, seismicity, geomorphometric modeling based on SRTM-90 m (slope, aspect, hillshade and elevation) and geophysical fields: geoid based on EGM-2008 and free-air Faye's gravity based on satellite derived gravity data from CryoSat-2 and Jason-1. In contrast to previous maps of Malawi, a scripting approach was introduced as a console-based cartographic mapping developed for plotting a series of thematic maps based on the high-resolution data. The maps demonstrate correlations between the topography and tectonic faults (Malawi Rift Zone) and earthquakes in the Malawi Lake and extent of landforms. The results demonstrate strong correspondence between the topography and geophysical fields (geoid and gravity): negative values of geoid (-15 to -20) are notable over the Malawi (Nyasa) Lake which corresponds with local topographic depressions. Free-air gravity fields reach the lowest values (-50 to -100) over the Malawi Lake. Local heights in gravity are compared with topographic mountain ranges in the NW and SW of the country on the borders with Zambia and Mozambique. The location of earthquakes vary with the majority located in the north. The geomorphological landforms demonstrate variability in slope steepness and aspect orientation shown on histogram. The techniques of scripts can be used to automatically map spatial data using raster datasets for geophysical visualization, and this paper demonstrated this through a variety of map from the presented thematic series of geophysical maps of Malawi. Full scripts used for mapping are available on the author's public GitHub repository with provided link to her open access codes.