GD Library - How to scale imported image

[CrimpJiggler]

I made this tool:

http://chemistryhelper.eu.pn/

with PHP and what I need it to be able to do now is to make some of the lobes grow or shrink. How I made this script is there is one script which loads single lobes from png and arranges them into a row like this:

then a second script loads the first one, and arranges the rows into a stack like this:

 

so I need to figure out how to make single lobes grow or shrink. Heres the script which loads the single lobes:

		mb_language('uni');
		mb_internal_encoding('UTF-8');

		header ("Content-type: image/png"); 
		$handle = ImageCreate ($this->img_width, $this->img_height) or die ("Cannot Create image"); 
		imagesetthickness($handle,3); 

		$lobe['color_one']['positive'] = imagecreatefrompng("$lobe_dir/lobe_u_$colors[0].png");
		$lobe['color_one']['negative'] = imagecreatefrompng("$lobe_dir/lobe_d_$colors[0].png");
		$lobe['color_two']['positive'] = imagecreatefrompng("$lobe_dir/lobe_u_$colors[1].png");
		$lobe['color_two']['negative'] = imagecreatefrompng("$lobe_dir/lobe_d_$colors[1].png");

		$bg_color = ImageColorAllocate ($handle, 255, 255, 255); 
		$line_color = ImageColorAllocate ($handle, 0, 0, 0); 




ImageLine($handle, $line_coords['x']['start'], $line_y_position, $line_coords['x']['end'], $line_y_position, $line_color);


		// merge the two images

		$lobe_y_offset = 28; 

		$height = $line_y_position - $lobe_y_offset;
		$low = $line_y_position + 2;
			
		$lobe_start = $line_coords['x']['start'];
		$increment = ($line_coords['x']['width'] / $this->lobe_num);


		for ($i=0; $i<$this->lobe_num; $i++) {
			
			$lobe_x_position = $lobe_start + ( $increment * $i ) + ( $increment / 4.2 );
			imagecopy($handle, $top_lobe, $lobe_x_position, $height, 0, 0, imagesx($top_lobe), imagesy($top_lobe)); 
			imagecopy($handle, $bottom_lobe, $lobe_x_position, $low, 0, 0, imagesx($bottom_lobe), imagesy($bottom_lobe)); 

		}

I removed a lot of code to make it quick to read, thats basically the part of the code which makes the straight line and adds 2 rows of lobes above and below it. To scale the lobes, I tried this:

		$percent = 0.5;

		// Get new sizes
		list($width, $height) = getimagesize("$lobe_dir/lobe_u_$colors[0].png");
		$newwidth = $width * $percent;
		$newheight = $height * $percent;

		// Load
		$thumb = imagecreatetruecolor($newwidth, $newheight);
        
		$lobe['color_one']['positive'] = imagecreatefrompng("$lobe_dir/lobe_u_$colors[0].png");
		$lobe['color_one']['negative'] = imagecreatefrompng("$lobe_dir/lobe_d_$colors[0].png");
		$lobe['color_two']['positive'] = imagecreatefrompng("$lobe_dir/lobe_u_$colors[1].png");
		$lobe['color_two']['negative'] = imagecreatefrompng("$lobe_dir/lobe_d_$colors[1].png");

		imagecopyresized($thumb, $lobe['color_one']['positive'], 0, 0, 0, 0, $newwidth, $newheight, $width, $height);

that should shrink one of the type of lobes to half its size, but it doesn't work, it doesn't change the size at all. 

[CrimpJiggler]

I figured out the first problem, so heres my second issue. I need to make the backgrounds of the lobes transparent,  so I added this code:

        imagealphablending($lobe['green']['negative'], true); // setting alpha blending on
        imagesavealpha($lobe['green']['negative'], true); 

and the problem is when I use a lobe with a transparent background, bugs start happening like this:

those lobes aren't supposed to be gray. I have no idea how that can even happen.