adding allele freq distribution in the plots

jeffersonfparil · Apr 17, 2024 · c6daaf7 · c6daaf7
1 parent 13b4807
commit c6daaf7
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Showing 9 changed files with 5,600 additions and 5,600 deletions.
diff --git a/res/cocksfoot-Concordance.svg b/res/cocksfoot-Concordance.svg
diff --git a/res/cocksfoot-Concordance_high_confidence_data.svg b/res/cocksfoot-Concordance_high_confidence_data.svg
diff --git a/res/cocksfoot-Mean_absolute_error.svg b/res/cocksfoot-Mean_absolute_error.svg
diff --git a/res/cocksfoot-Mean_absolute_error_high_confidence_data.svg b/res/cocksfoot-Mean_absolute_error_high_confidence_data.svg
diff --git a/res/grape-Concordance.svg b/res/grape-Concordance.svg
diff --git a/res/grape-Mean_absolute_error.svg b/res/grape-Mean_absolute_error.svg
diff --git a/res/perf_plot.R b/res/perf_plot.R
@@ -139,7 +139,7 @@ plot_metrics = function(df, dataset, vec_2_metrics=c("mae_frequencies", "concord
     q = seq(0, 1, by=0.1)
     for (algo in vec_algorithm) {
       # algo = vec_algorithm[1]
-      par(mar=c(5,5,1,1))
+      par(mar=c(5,5,1,6))
       idx_col_mae = which(grepl("^mae_", colnames(subdf)))
       plot(x=c(0,1), y=range(subdf[, idx_col_mae], na.rm=TRUE), type="n", xlab="Observed allele frequencies (5% MAF)", ylab="Imputation error\n(mean absolute error)", main=algo, las=1)
       colour = vec_colours[vec_algorithm==algo]
@@ -191,7 +191,7 @@ plot_metrics = function(df, dataset, vec_2_metrics=c("mae_frequencies", "concord
       colour = vec_colours[vec_algorithm==algo]
       idx_col = which(grepl("var_x_mae_", colnames(subdf)))
       n_bins = length(idx_col) / 2
-      par(mar=c(5,5,1,1))
+      par(mar=c(5,5,1,6))
       idx_temp = which(subdf$algo == algo) 
       y_temp = data.frame(y=unlist(subdf[idx_temp, idx_col[seq(2, length(idx_col), by=2)]]), b=rep(1:n_bins, each=length(idx_temp)), m=rep(subdf$missing_rate[idx_temp], time=n_bins))
       y_temp = aggregate(y ~ b + m, data=y_temp, FUN=mean, na.rm=TRUE)[,3]

diff --git a/res/soybean-Concordance.svg b/res/soybean-Concordance.svg
diff --git a/res/soybean-Mean_absolute_error.svg b/res/soybean-Mean_absolute_error.svg