Commit 65e3b4e2 authored by Kunst, Jonathan's avatar Kunst, Jonathan
Browse files

Extended lodmod df to create extra information on tooltip

parent 8cef877d
......@@ -49,65 +49,6 @@ plotQTL(LOD_data = qtl_LODs.4x,
plotLinearQTL(LOD_data = qtl_LODs.4x,
col = "dodgerblue")
# plotly example
dfs <- qtl_LODs.4x$QTL.res %>%
nest_by(chromosome)
lapply(seq_along(dfs$data), function(i){
plot_ly(dfs$data[[i]], x = ~position, y = ~LOD, type = 'scatter', mode = 'lines') %>%
layout(yaxis = list(title = 'Logarithm of Odds (LOD)', showgrid = FALSE),
xaxis = list(title = str(i), showgrid = FALSE))
}) %>%
subplot(., shareX = FALSE, shareY = TRUE, titleX = TRUE)
panel <- . %>%
plot_ly(x = ~position, y = ~LOD) %>%
add_lines() %>%
add_annotations(
text = ~unique(chromosome),
x = 0.5,
y = 0,
yref = "paper",
xref = "paper",
yanchor = "bottom",
xanchor = 'center',
yshift = -35,
showarrow = FALSE,
font = list(size = 15)
) %>%
layout(
showlegend = TRUE,
shapes = list(
type = "rect",
x0 = 0,
x1 = 1,
xref = "paper",
y0 = 0,
y1 = 0,
yanchor = 'center',
yref = "paper",
ysizemode = "pixel",
fillcolor = toRGB("gray80"),
line = list(color = "transparent")
),
xaxis = list(showgrid = FALSE),
yaxis = list(showgrid = FALSE)
)
qtl_LODs.4x$QTL.res %>%
mutate(chromosome = paste('Linkage Group', chromosome)) %>%
group_by(chromosome) %>%
do(p = panel(.)) %>%
subplot(nrows = 1, shareX = FALSE, shareY = TRUE)
plot_ly(qtl_LODs.4x$QTL.res,
x = ~position,
y = ~LOD)
# sig thresholds with permutation tests
qtl_LODs.4x <- QTLscan(IBD_list = IBD_4x,
Phenotype.df = Phenotypes_4x,
......@@ -217,9 +158,11 @@ lodsmod2 <- lodsmod1 %>%
LOD = jitter(LOD, 1, 0.25),
.keep = 'unused')
lodsmod <- rbind(lodsmod1, lodsmod2)
lodsmod <- rbind(lodsmod1, lodsmod2) %>%
left_join(bind_rows(phased_maplist.4x), by = 'position')
p <- ggplot(lodsmod, aes(x = position, y = LOD, color = model)) +
p <- ggplot(lodsmod, aes(x = position, y = LOD, color = model, linetype = model)) +
geom_line() +
facet_grid(~chromosome,
switch = 'x',
......
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