Is the 1st plot in plot(pc$U) the same as plot(pc$au[,1])?
Comments (5)
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reporter Thank you Xin-Qiu. My protein has 442 residues.
Both
dim(pc$au[, 1])
anddim(pc$au[, 1])
giveNULL
, forlength
:> length(pc$au[, 1]) [1] 442 > length(pc$U[, 1]) [1] 1326
So the
pc$U[, 1]
shows all the x,y,z coordinates for the 442 alpha-carbons (3*442 = 1326). However,Index Number
of 1-442 is used forplot(pc$U)
. Do you know how to plot each of theplot(pc$U)
? I triedplot(pc$U[,1])
, but theIndex Number
is 1-1326, not normalised to atom index (i.e. 1-442). -
reporter Hi Xin-Qiu, could you please help me this?
Also, can I clarify that
dim(pc$U)
returns1326 1326
. So the 1326 rows are the contribution of x, y, z of the 442 alpha-carbon, while 1326 columns are the 1326 PCs, is that correct? -
Yes, all your thoughts about the dimension of
pc$U
are correct.If you want residue wise plot, you should use
pc$au
instead ofpc$U
. -
reporter - changed status to resolved
I think I understand it, but it is still unclear how to specifically only plot the first image of plot(pc$U), so that I can plot other graphs of PC vs residue-indices (e.g. PC5 vs residue-indices)
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No, they are not the same. If you check dimensions you can clearly see they are different:
dim(pc$au[, 1])
,dim(pc$U[, 1])
.