Make cleaning
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Eric Coissac committed
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19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 1Line truncated
|
||||
"z": [-1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1000000000000001, -1.1599999999999999, -1.2, -1.24, -1.27, -1.3, -1.3200000000000001, -1.3300000000000001, -1.3400000000000001, 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truncated
|
||||
"type": "mesh3d",
|
||||
"frame": null
|
||||
}
|
||||
],
|
||||
"highlight": {
|
||||
"on": "plotly_click",
|
||||
"persistent": false,
|
||||
"dynamic": false,
|
||||
"selectize": false,
|
||||
"opacityDim": 0.20000000000000001,
|
||||
"selected": {
|
||||
"opacity": 1
|
||||
},
|
||||
"debounce": 0
|
||||
},
|
||||
"shinyEvents": ["plotly_hover", "plotly_click", "plotly_selected", "plotly_relayout", "plotly_brushed", "plotly_brushing", "plotly_clickannotation", "plotly_doubleclick", "plotly_deselect", "plotly_afterplot", "plotly_sunburstclick"],
|
||||
"base_url": "https://plot.ly"
|
||||
}
|
||||
+149
@@ -0,0 +1,149 @@
|
||||
---
|
||||
title: "Untitled"
|
||||
format: html
|
||||
editor: visual
|
||||
---
|
||||
|
||||
```{r}
|
||||
library(tidyverse)
|
||||
library(plotly)
|
||||
library(matrixStats)
|
||||
```
|
||||
|
||||
```{r}
|
||||
log_sum_exp <- function(a,b) {
|
||||
m <- map2_dbl(a,b,max)
|
||||
m + log(exp(a-m)+exp(b-m))
|
||||
}
|
||||
```
|
||||
|
||||
$$
|
||||
\log(1 - e^b) = \log\left(-e^{(1-b)}\right)
|
||||
$$
|
||||
|
||||
```{r}
|
||||
log1m_exp <- function(b) {
|
||||
if (any(b >= 0)) {
|
||||
stop(glue::glue("b must be negative (b={b})"))
|
||||
}
|
||||
return(log(-expm1(b))) # expm1(b) = exp(b) - 1, pour éviter les erreurs d'arrondi
|
||||
}
|
||||
```
|
||||
|
||||
$$
|
||||
\log(e^a - e^b) = a + \log(1 - e^{b-a})
|
||||
$$
|
||||
|
||||
```{r}
|
||||
log_diff_exp <- function(a, b) {
|
||||
# Vérifier si a > b pour éviter des résultats indéfinis
|
||||
if (any(a < b)) {
|
||||
stop(glue::glue("Erreur : a ({a}) doit etre strictement sup�rieur � b ({b}) pour que e^a - e^b soit positif."))
|
||||
}
|
||||
|
||||
# Calculer log(e^a - e^b) de manière stable
|
||||
ifelse(a == b, -Inf,a + log1m_exp(b-a))
|
||||
}
|
||||
```
|
||||
|
||||
$$
|
||||
P_{error} = 10^{-\frac{Q}{10}}
|
||||
$$
|
||||
|
||||
$$
|
||||
\begin{aligned}
|
||||
q_F &= -\frac{Q_F}{10} \cdot \log(10) \\
|
||||
q_R &= -\frac{Q_R}{10} \cdot \log(10) \\
|
||||
P(macth | Obs(match)) &= (1-e^{q_F}) (1-e^{q_R}) + (1-e^{q_F})\frac{e^{q_R}}{4}+ (1-e^{q_R})\frac{e^{q_F}}{4} + \frac{e^{q_F+q_R}}{4} \\
|
||||
&=1 - e^{q_R} - e^{q_F} + e^{q_F+q_R} + \frac{e^{q_R}}{4} - \frac{e^{q_F+q_R}}{4} + \frac{e^{q_F}}{4} - \frac{e^{q_F+q_R}}{4} + \frac{e^{q_F+q_R}}{4} \\
|
||||
&= \frac{4 - 4e^{q_F} - 4e^{q_R} + 4e^{q_F+q_R} + e^{q_F} + e^{q_R} - e^{q_F+q_R}}{4} \\
|
||||
&= \frac{4 - 3e^{q_F}- 3e^{q_R} + 3e^{q_F+q_R}}{4}\\
|
||||
&= \frac{4 - 3(e^{q_F}+e^{q_R}-e^{q_F+q_R})}{4} \\
|
||||
&= 1 - \frac{3}{4}\left(e^{q_F}+e^{q_R}-e^{q_F+q_R}\right)
|
||||
\end{aligned}
|
||||
$$
|
||||
|
||||
```{r}
|
||||
Pm_match_observed <- function(Q_F, Q_R) {
|
||||
l10 <- log(10)
|
||||
l3 <- log(3)
|
||||
l4 <- log(4)
|
||||
|
||||
q_F <- -Q_F/10*l10
|
||||
q_R <- -Q_R/10*l10
|
||||
|
||||
term1 <- log_sum_exp(q_F,q_R)
|
||||
term2 <- log_diff_exp(term1,q_F+q_R) + l3 - l4
|
||||
|
||||
log1m_exp(term2)
|
||||
}
|
||||
```
|
||||
|
||||
$$
|
||||
\begin{aligned}
|
||||
P(macth | Obs(mismatch)) &= \frac{(1-e^{q_F})e^{q_R}}{4} + \frac{(1-e^{q_R})e^{q_F}}{4} + \frac{e^{q_F+q_R}}{4} \\
|
||||
&= \frac{(1-e^{q_F})e^{q_R} + (1-e^{q_R})e^{q_F} + e^{q_F+q_R}}{4} \\
|
||||
&= \frac{e^{q_R} - e^{q_F+q_R} + e^{q_F} - e^{q_F+q_R} + e^{q_F+q_R}}{4} \\
|
||||
&= \frac{e^{q_F} + e^{q_R} - e^{q_F+q_R}}{4}
|
||||
\end{aligned}
|
||||
$$
|
||||
|
||||
```{r}
|
||||
Pm_mismatch_observed <- function(Q_F, Q_R) {
|
||||
l10 <- log(10)
|
||||
l3 <- log(3)
|
||||
l4 <- log(4)
|
||||
|
||||
q_F <- -Q_F/10*l10
|
||||
q_R <- -Q_R/10*l10
|
||||
|
||||
term1 <- log_sum_exp(q_F,q_R)
|
||||
log_diff_exp(term1,q_F+q_R) - l4
|
||||
}
|
||||
```
|
||||
|
||||
```{r}
|
||||
score_match_observed <- function(Q_F, Q_R) {
|
||||
Pm_match_observed(Q_F,Q_R) - log1m_exp(Pm_match_observed(Q_F,Q_R))
|
||||
}
|
||||
|
||||
score_mismatch_observed <- function(Q_F, Q_R) {
|
||||
Pm_mismatch_observed(Q_F,Q_R) - log1m_exp(Pm_mismatch_observed(Q_F,Q_R))
|
||||
}
|
||||
```
|
||||
|
||||
```{r}
|
||||
scores <- expand_grid(QF=0:40,QR=0:40) %>%
|
||||
mutate(score_match_observed = round(score_match_observed(QF,QR),2),
|
||||
score_mismatch_observed = round(score_mismatch_observed(QF,QR),2))
|
||||
```
|
||||
|
||||
```{r}
|
||||
plot_match <- plot_ly(scores,
|
||||
x=~QF, y=~QR, z=~score_match_observed,
|
||||
type="mesh3d") %>%
|
||||
layout(
|
||||
plot_bgcolor = "#bababa",
|
||||
scene = list(
|
||||
xaxis = list(title = "Q forward read"), # Change x/y/z axis title
|
||||
yaxis = list(title = "Q reverse read"),
|
||||
zaxis = list(title = "Score match")))
|
||||
```
|
||||
|
||||
```{r}
|
||||
plot_mismatch <- plot_ly(scores,
|
||||
x=~QF, y=~QR, z=~score_mismatch_observed,
|
||||
type="mesh3d") %>%
|
||||
layout(
|
||||
plot_bgcolor = "#bababa",
|
||||
scene = list(
|
||||
xaxis = list(title = "Q forward read"), # Change x/y/z axis title
|
||||
yaxis = list(title = "Q reverse read"),
|
||||
zaxis = list(title = "Score mismatch")))
|
||||
```
|
||||
|
||||
```{r}
|
||||
write(plotly_json(plot_match,FALSE),"content/docs/commands/alignments/obipairing/exact-alignment/match.json")
|
||||
write(plotly_json(plot_mismatch,FALSE),"content/docs/commands/alignments/obipairing/exact-alignment/mismatch.json")
|
||||
|
||||
```
|
||||
Reference in new issue
Block a user