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The pixels array is stored in the "data" attribute of Mat. Let's suppose that we have a Mat Matrix where each pixel has 3 bytes (CV_8UC3).

For this example, let's draw a RED pixel at position 100x50.

Mat foo;
int x=100, y=50;

Solution 1:

Create a macro function that obtains the pixel from the array.

#define PIXEL(frame, W, x, y) (frame+(y)*3*(W)+(x)*3)
//...
unsigned char * p = PIXEL(foo.data, foo.rols, x, y);
p[0] = 0;   // B
p[1] = 0;   // G
p[2] = 255; // R

Solution 2:

Get's the pixel using the method ptr.

unsigned char * p = foo.ptr(y, x); // Y first, X after
p[0] = 0;   // B
p[1] = 0;   // G
p[2] = 255; // R