| plot_compare_profiles {MutationalPatterns} | R Documentation |
Plots two 96 mutation profiles and their difference, reports the residual sum of squares (RSS).
plot_compare_profiles(profile1, profile2, profile_names = c("profile 1",
"profile 2"), profile_ymax = 0.2, diff_ylim = c(-0.02, 0.02), colors,
condensed = FALSE)
profile1 |
First 96 mutation profile |
profile2 |
Second 96 mutation profile |
profile_names |
Character vector with names of the mutations profiles used for plotting, default = c("profile 1", "profile 2") |
profile_ymax |
Maximum value of y-axis (relative contribution) for profile plotting, default = 0.2 |
diff_ylim |
Y-axis limits for profile difference plot, default = c(-0.02, 0.02) |
colors |
6 value color vector |
condensed |
More condensed plotting format. Default = F. |
96 spectrum plot of profile 1, profile 2 and their difference
mut_matrix,
extract_signatures
## See the 'mut_matrix()' example for how we obtained the following
## mutation matrix.
mut_mat <- readRDS(system.file("states/mut_mat_data.rds",
package="MutationalPatterns"))
## Extracting signatures can be computationally intensive, so
## we use pre-computed data generated with the following command:
# nmf_res <- extract_signatures(mut_mat, rank = 2)
nmf_res <- readRDS(system.file("states/nmf_res_data.rds",
package="MutationalPatterns"))
## Compare the reconstructed 96-profile of sample 1 with orignal profile
plot_compare_profiles(mut_mat[,1],
nmf_res$reconstructed[,1],
profile_names = c("Original", "Reconstructed"))