diff --git a/template.qmd b/template.qmd index e60f8e5..c71aa25 100644 --- a/template.qmd +++ b/template.qmd @@ -178,7 +178,7 @@ blue line shows the linear model fit.](`r params$fig_cor_snp`){#fig-fig_cor_snp} ### Description for intra-host nucleotide variants A total of `r n_SNV` different single nucleotide variants (SNV) and `r n_INDELS` -INDELs have been detected along the genome (@fig-SNV). +insertions and deletions (indels) have been detected along the genome (@fig-SNV). ::: {.panel-tabset} @@ -225,11 +225,12 @@ frequencies in time for a given genome position.](`r params$panel`){#fig-panel} ### Correlation between alternative alleles To detect possible interactions between mutations, pairwise correlation between allele -frequencies are calculated and shown in @fig-heatmap. This heatmap is an interactive figure in which it is posible to zoom in specific regions. +frequencies are calculated (@fig-heatmap). The heatmap is an interactive figure that allows +zooming in on specific regions. ```{r heatmap, echo = F, message = F, fig.align = 'center'} #| label: fig-heatmap -#| fig-cap: "Hierarchically clustered heatmap of the pairwise Pearson’s correlation coefficients between the time series of allele frequencies in the case study." +#| fig-cap: "Interactive hierarchically clustered heatmap of the pairwise Pearson’s correlation coefficients between the time series of allele frequencies in the case study." heatmaply_cor( cor.mat, @@ -241,18 +242,17 @@ heatmaply_cor( ### Non-synonymous to synonymous rate ratio over time -To track selection footprints, the substitutions per synonymous site (dS) and -per non-synonymous site (dN) for each sample with respect to the reconstructed -ancestral sequence have been calculated (@fig-evo). Also $\omega$ (dN/dS) is shown in @fig-omega. +To track selection footprints, the substitutions per synonymous site ($dS$) and +per non-synonymous site ($dN$) for each sample with respect to the reconstructed +ancestral sequence have been calculated (@fig-evo), as well as their ratio ($\omega = dN/dS$; @fig-omega). ::: {.panel-tabset} ## dN and dS ![Time series of dN and dS. Each point corresponds to a different sample, sorted in chronological order.](`r params$evo`){#fig-evo} -## $\omega$ (dN /dS) +## $\omega$ ($dN/dS$) -![Time series of $\omega$ (dN/dS). Each point corresponds to a different sample, sorted in chronological order.](`r params$omega_plot`){#fig-omega} +![Time series of $\omega$ ($dN/dS$). Each point corresponds to a different sample, sorted in chronological order.](`r params$omega_plot`){#fig-omega} ::: -