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Plotting same dataset results in different outputs

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The file GMD_F16.dat has 1000 2D points, so 1000 rows & 2 col data.
The output seems different when plotting with for loop & when plotting within entire range, PFB commands & sample code for reference.
Plotting with For loop
subplot(1,4,1) for i = 1:rows plot(data1(i,1),data1(i,2),'k.') hold on end title('Original Data');
Plotting within entire range
subplot(1,4,3) plot(data1(:,1),data1(:,2),'k.','MarkerSize',12)
Please guide.

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