is there any way to select a subplot in gnuplot's multiplot mode as in subplot(n,m,x) in Matlab where x is the one I want to plot at? I am plotting three points using linespoints on a graph in red color at first, then I want to plot a single point in black, not connected by lines to any other points.
I think you might be mixing things. Multiplot will generate several graphs on the same page, but you are talking about plotting more than once on one of them.
The answer to your question on selecting one of the plotting areas is no, you cannot freely select one arbitrarily, unless you manually set the size and the origin. Otherwise, if you use the layout option, you would need to select the order in which the plots get filled rows first, columns first, downwards or upwards.
Imagine you have a 3x3 layout and you want the graph in the middle to be plotted first. Then you will need to do something along these lines:
set multiplot
set size 1./3.,1./3.
set origin 1./3.,1./3.
plot sin(x)

However, I suspect you simply want to plot several times on the same graph. To do that, separate files or functions with a comma within the same plot command. For instance, plot sin(x) on a graph on the left and cos(x) and sin(x) on the graph on the right in a 1x2 layout (the default is to fill from left to right):
set multiplot layout 1,2
plot sin(x)
plot sin(x), cos(x)

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