Description Usage Arguments Details Author(s) Examples
The k-mer grid pyramid 3D plotting function allows to plot the k-mer distribution given by a window of a single sequences. Further, it is possible to compare two sequences to each other.
1 2 |
list |
List of sequences generated by the function
|
color |
Single value 'black', if all points should be black or vector of length nrow(df) if all points should be colored differently. |
difference |
Should the difference between two list entries be calcualted and the difference pyramid be plotted? [default = FALSE] |
identify |
Set to TRUE, if points should be identified, than the k-mer will be shown. |
bw |
Black and white plot for the differences [default = FALSE] |
bw.cex |
Size of the text symbols in the black and white difference plot. |
edges |
A vector of edges which should be printed. Because there is no difference between AG and GA only the alpha numeric one will work: AG. |
The function plots the k-mer distribution of single sequences
generated by the function link{get_pca_window_list}
into
the three dimensional space of a principal component analysis.
The user can provide single list entries or two list entries. In the first case the k-mer distribution given by the window size will be plotted. The color and can be changed by color or different edges can be shown by edges. If two list entries are supplied and difference is set to TRUE the difference in both sequences given the window k-mer count is calculated and shown by different radius sizes. An increase from sequence one to sequence two is colored blue and a decrease is colored red. The identify option allows to identify single points in the 3D plot.
Jochen Kruppa
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 | ## Read in own DNA sequences by the package Biostrings (see Details for more information)
data(viralExampleSeqs)
viral_window_list <- get_pca_window_list(viralExampleSeqs, window = 2)
pyramid_3d_grid(viral_window_list[1],
color = "red")
pyramid_3d_grid(viral_window_list[1],
color = "red",
identify = TRUE)
pyramid_3d_grid(viral_window_list[c(3,5)],
difference = TRUE,
identify = TRUE)
pyramid_3d_grid(viral_window_list[c(3,5)],
difference = TRUE,
bw = TRUE,
bw.cex = 75,
identify = TRUE)
pyramid_3d_grid(viral_window_list[1],
color = "red",
edges = c("AT", "CG"))
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