library("vcfR") library(adegenet) library("LEA") setwd ("/Users/tacatanach/Desktop/Manuscripts_Proposals/SSHA/snmf/") SSHA <- read.lfmm("snp_must_have_nisus_no_toepads_convert_lfmm_no_constant_reorder_no_nisus.lfmm") SSHA lfmm2geno("snp_must_have_nisus_no_toepads_convert_lfmm_no_constant_reorder_no_nisus.lfmm", output.file = "snp_must_have_nisus_no_toepads_convert_lfmm_no_constant_reorder_no_nisus_geno.geno", force = TRUE) #now you have .geno file ## ## https://www.rdocumentation.org/packages/LEA/versions/1.4.0/topics/snmf ########## snmf crashes in RStudio but doesnt through a terminal window #### project = NULL project = snmf("snp_must_have_nisus_no_toepads_convert_lfmm_no_constant_reorder_no_nisus_geno.geno", K=1:10, entropy = TRUE, repetitions = 10, project = "new") plot(project, col = "blue", pch = 19, cex = 1.2) pc = pca("snp_must_have_nisus_no_toepads_convert_lfmm_no_constant_reorder_no_nisus_geno.geno", scale = TRUE) tw = tracy.widom(pc) tw$pvalues[1:10] plot(tw$percentage) best = which.min(cross.entropy(project, K = 2)) my.colors <- c("black", "blue") barchart(project, K = 2, run = best, border = NA, space = 0, col = my.colors, xlab = "Individuals", ylab = "Ancestry proportions", main = "Ancestry matrix") -> bp axis(1, at = 1:length(bp$order), labels = bp$order, las=1, cex.axis = .4) best = which.min(cross.entropy(project, K = 3)) my.colors <- c("black", "blue", "yellow") barchart(project, K = 3, run = best, border = NA, space = 0, col = my.colors, xlab = "Individuals", ylab = "Ancestry proportions", main = "Ancestry matrix") -> bp axis(1, at = 1:length(bp$order), labels = bp$order, las=1, cex.axis = .4) best = which.min(cross.entropy(project, K = 4)) my.colors <- c("black", "darkgreen", "blue", "yellow") barchart(project, K = 4, run = best, border = NA, space = 0, col = my.colors, xlab = "Individuals", ylab = "Ancestry proportions", main = "Ancestry matrix") -> bp axis(1, at = 1:length(bp$order), labels = bp$order, las=1, cex.axis = .4) best = which.min(cross.entropy(project, K = 5)) my.colors <- c("lightblue","black", "green", "purple", "gold") barchart(project, K = 5, run = best, border = NA, space = 0, col = my.colors, xlab = "Individuals", ylab = "Ancestry proportions", main = "Ancestry matrix") -> bp axis(1, at = 1:length(bp$order), labels = bp$order, las=1, cex.axis = .4) best = which.min(cross.entropy(project, K = 6)) my.colors <- c("blue", "lightblue", "green", "black", "purple", "gold") barchart(project, K = 6, run = best, border = NA, space = 0, col = my.colors, xlab = "Individuals", ylab = "Ancestry proportions", main = "Ancestry matrix") -> bp axis(1, at = 1:length(bp$order), labels = bp$order, las=1, cex.axis = .4) best = which.min(cross.entropy(project, K = 7)) my.colors <- c("red", "lightblue", "gray", "gold", "purple", "green", "black") barchart(project, K = 7, run = best, border = NA, space = 0, col = my.colors, xlab = "Individuals", ylab = "Ancestry proportions", main = "Ancestry matrix") -> bp axis(1, at = 1:length(bp$order), labels = bp$order, las=1, cex.axis = .4) ########## snmf crashes in RStudio but doesnt through a terminal window ####