The Raman scattering spectra (RS) of two series of monolayer graphene samples irradiated with various doses of C$^{+}$ and Xe$^{+}$ ions were measured after annealing in high vacuum, and in forming gas (95%Ar+5%H$_{2}$). It was found that these methods of annealing have dramatically different influence on the RS lines. Annealing in vacuum below 500$^{circ}$C leads to significant decrease of both D-line, associated with defects, and 2D-line, associated with the intact lattice structure, which can be explained by annealing-induced enhanced doping. Further annealing in vacuum up to 1000$^{circ}$C leads to significant increase of 2D-line together with continuous decrease of D-line, which gives evidence of partial removal of defects and recovery of the damaged lattice. Annealing in forming gas is less effective in this sense. The blue shift of all lines is observed after annealing. It is shown that below 500$^{circ}$C, the unintentional doping is the main mechanism of shift, while at higher annealing temperatures, the lattice strain dominates due to mismatch of the thermal expansion coefficient of graphene and the SiO$_{2}$ substrate. Inhomogeneous distribution of stress and doping across the samples leads to the correlated variation of the amplitude and the peak position of RS lines.
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