Yama considers Rui's entire existence to be a moment of heartwarming, literally, as he thinks that everything about her exudes "warmth", down to her hair and eye color. Rui spends a lot of time looking after Yama, and she's the reason Yama's even alive, as Yama almost killed himself after Misaki moved away; Rui had to coax Yama away from the brink. In the ending, she even patiently spends a few months helping Yama with his therapy so he can leave the hospital as soon as possible.
On another Rui-related note, Yama thinks Rui might have a crush on him, but he isn't sure whether that's really the case or whether she only likes him because they've spent so much time together. At one point, we very briefly play as Rui, and we find out yes, she does have a crush on him, as she thinks he's very attractive. In fact, for this reason Rui isn't even all that mad at Yama after their fight, despite Yama being torn up with guilt about it.
Misaki will sometimes give Yama pep talks on how he shouldn't be so down on himself, as Misaki thinks Yama's really cool. This is especially notable because the only other girl who openly says she thinks Yama is cool is his childhood friend Rui.
If Yama invites Elizabeth into his apartment after Yama is considered a murder suspect, Elizabeth will say something unexpectedly nice, given her usual antagonistic relationship to Yama: Elizabeth thinks Yama is incompetent, which is exactly what makes Elizabeth think Yama can't be the murderer; do the police really believe Yama of all people is capable of concocting a genius plan to not only murder students but outwit the cops while he's at it? Yama is surprised at Elizabeth's unexpected faith in him.
