diff --git a/src/harpy/reports/AlignStats.Rmd b/src/harpy/reports/AlignStats.Rmd index 9874c741f..1007901c3 100644 --- a/src/harpy/reports/AlignStats.Rmd +++ b/src/harpy/reports/AlignStats.Rmd @@ -128,7 +128,7 @@ hs <- hist( breaks = min(valids$reads):max(valids$reads), plot = F ) -hs$counts <- round(hs$counts / sum(hs$counts) * 100, 2) +hs$counts <- round(hs$counts / sum(hs$counts) * 100, 4) hs <- data.frame(val = hs$breaks[-1], freq = hs$counts) hchart(hs, "areaspline", hcaes(x = val, y = freq), color = "#8484bd", name = "% of molecules", marker = list(enabled = FALSE)) |> @@ -145,7 +145,7 @@ hchart(hs, "areaspline", hcaes(x = val, y = freq), color = "#8484bd", name = "% ### bases per {.no-title} ```{r basesper, echo = FALSE, message = FALSE, warning = FALSE, out.width="100%"} hs <- hist(round(valids$aligned_bp, -2), breaks = 50, plot = F) -hs$counts <- round(hs$counts / sum(hs$counts)*100,2) +hs$counts <- round(hs$counts / sum(hs$counts)*100,4) hs <- data.frame(val = hs$breaks[-1], freq = hs$counts) hchart(hs, "areaspline", hcaes(x = val, y = freq), color = "#75b89e", name = "% of molecules", marker = list(enabled = FALSE)) |> @@ -159,7 +159,6 @@ hchart(hs, "areaspline", hcaes(x = val, y = freq), color = "#75b89e", name = "% ) ``` - ## inferred-header ### inferred desc {.no-title}

Inferred Molecule Lengths

@@ -212,12 +211,13 @@ molecule coverage as `300bp รท molecule_length`, whereas the plot on the right c ### coverage by aligned bp {.no-title} ```{r inferred_cov_bp, echo = FALSE, message = FALSE, warning = FALSE, out.width = '100%'} +#TODO THIS IS BROKEN hs <- hist( - round(valids$percent_coverage, 0), - breaks = seq(0, round(max(valids$coverage_bp + 1, 0)), by = 1), + round(valids$coverage_bp, 0), + breaks = seq(0, 1, by = 0.05), plot = F ) -hs$counts <- round(hs$counts / sum(hs$counts)*100,2) +hs$counts <- round(hs$counts / sum(hs$counts)*100,4) hs <- data.frame(val = hs$breaks[-1], freq = hs$counts) hchart(hs, "areaspline", hcaes(x = val, y = freq), color = "#e59765", name = "% of molecules", marker = list(enabled = FALSE)) |> @@ -234,8 +234,8 @@ hchart(hs, "areaspline", hcaes(x = val, y = freq), color = "#e59765", name = "% ### coverage by inserts {.no-title} ```{r inferred_cov_insert, echo = FALSE, message = FALSE, warning = FALSE, out.width = '100%'} hs <- hist( - round(valids$percent_coverage, 0), - breaks = seq(0, round(max(valids$coverage_inserts + 1, 0)), by = 1), + round(valids$coverage_inserts, 0), + breaks = seq(0, 1, by = 0.05), plot = F ) hs$counts <- round(hs$counts / sum(hs$counts)*100,2)