Commit d23e22f2 authored by Midoux Cedric's avatar Midoux Cedric

Merge branch 'master' into glomTable

parents a949d8e1 0dffda34
File added
......@@ -19,10 +19,9 @@
## Happy path: excel version
if (input$CSVsep == "excel") {
## For efficiency and consistency, maybe replace with readr::read_xl
sdf <- RcmdrMisc::readXL(input$fileMeta$datapath,
rownames = TRUE,
header = TRUE)
sdf <- as.data.frame(readxl::read_excel(input$fileMeta$datapath))
row.names(sdf) <- sdf[, 1]
sdf <- sdf[, -1]
sdf$SampleID <- rownames(sdf)
return(sdf)
}
......
library(microbenchmark)
mb <- microbenchmark::microbenchmark(
"clear" = {
rm(list = ls())
lapply(paste('package:', names(sessionInfo()$otherPkgs), sep=""), detach, character.only=TRUE, unload=TRUE)
},
"load packages" = {
library(shinydashboard)
library(glue)
source("https://raw.githubusercontent.com/mahendra-mariadassou/phyloseq-extended/master/R/load-extra-functions.R")
source("internals.R")
},
"load demo Chailloux" = {
load("demo/demo.RData")
data <- get("food")
},
"barplot" = {
p <- plot_bar(physeq = data, fill = "Phylum", x = "Description", title = "OTU abundance barplot")
p <- p + facet_grid(". ~ EnvType", scales = "free_x")
plot(p)
},
"filtered plot" = {
p <- plot_composition(physeq = data, taxaRank1 = "Kingdom", taxaSet1 = "Bacteria", taxaRank2 = "Phylum", numberOfTaxa = 10, fill = "Phylum", x = "Description")
p <- p + facet_grid(". ~ EnvType", scales = "free_x")
plot(p)
},
"heatmap" = {
p <- plot_heatmap(prune_taxa(names(sort(taxa_sums(data), decreasing = TRUE)[1:250]), data), distance = "bray", method = "NMDS", low = "yellow", high = "red", na.value = "white", sample.order = "Description", title = "Taxa heatmap by samples")
p <- p + facet_grid(". ~ EnvType", scales = "free_x")
plot(p)
},
"alpha" = {
p <- plot_richness(physeq = data, measures = c("Observed", "Chao1", "ACE", "Shannon", "Simpson", "InvSimpson", "Fisher"), x = "EnvType", color = "EnvType", shape = "FoodType", title = "Alpha diversity graphics")
p <- p + geom_boxplot()
p <- p + geom_point()
plot(p)
},
"beta" = {
beta <- melt(as(distance(data, method = "bray"), "matrix"))
colnames(beta) <- c("x", "y", "distance")
new_factor = as.factor(get_variable(data, "EnvType"))
variable_sort <- as.factor(get_variable(data, "EnvType")[order(new_factor)])
L = levels(reorder(sample_names(data), as.numeric(new_factor)))
beta$x <- factor(beta$x, levels = L)
beta$y <- factor(beta$y, levels = L)
palette <- hue_pal()(length(levels(new_factor)))
tipColor <- col_factor(palette, levels = levels(new_factor))(variable_sort)
p1 <- ggplot(beta, aes(x = x, y = y, fill = distance))
p1 <- p1 + geom_tile()
p1 <- p1 + ggtitle("Beta diversity heatmap")
p1 <- p1 + theme(axis.text.x = element_text(angle = 90, hjust = 1, color = tipColor), axis.text.y = element_text(color = tipColor), axis.title.x = element_blank(), axis.title.y = element_blank())
plot(p1 + scale_fill_gradient2())
},
"rarefaction" = {
p <- ggrare(physeq = data, step = 100, se = FALSE, color = "EnvType", label = "Description")
p <- p + facet_grid(". ~ FoodType")
p <- p + geom_vline(xintercept = min(sample_sums(data)), color = "gray60")
p <- p + ggtitle("Rarefaction curves")
plot(p)
},
"acp" = {
p <- plot_samples(physeq = data, ordination = ordinate(data, method = "MDS", distance = "unifrac"), axes = c(1, 2), color = "EnvType", shape = "FoodType", replicate = "EnvType", label = "Description", title = "Samples ordination graphic")
p <- p + stat_ellipse(aes_string(group = "EnvType"))
plot(p + theme_bw())
},
"tree" = {
p <- plot_tree(physeq = prune_taxa(names(sort(taxa_sums(data), decreasing = TRUE)[1:20]), data), method = "sampledodge", color = "EnvType", size = "abundance", label.tips = "taxa_names", sizebase = 5, ladderize = "left", plot.margin = 0, title = "Phylogenetic tree")
plot(p)
},
"clustering" = {
p <- plot_clust(physeq = data, dist = "unifrac", method = "ward.D2", color = "EnvType")
plot(p)
},
times = 100, unit = "s", control = list(order="inorder"))
mb
save(mb, file = "benchmark.RData")
mb_plot <- microbenchmark::autoplot.microbenchmark(mb)
ggsave("benchmark.png", plot = mb_plot)
This diff is collapsed.
......@@ -83,6 +83,7 @@ shinyUI(dashboardPage(
tabPanel(
"Summary",
verbatimTextOutput("phyloseqPrint"),
uiOutput("sampledataTable"),
withLoader(uiOutput("summaryTable")),
tags$footer(
"Questions, problems or comments regarding this application should be sent to ",
......@@ -103,17 +104,8 @@ shinyUI(dashboardPage(
uiOutput("histUI")),
tabPanel(
"Filtered barplot",
withLoader(plotOutput("histoFocus", height = 700)),
box(
title = "Paramètres",
width = NULL,
status = "primary",
uiOutput("histFocusUIfocusRank"),
uiOutput("histFocusUIfocusTaxa"),
uiOutput("histFocusUIfocusNbTaxa"),
uiOutput("histFocusUIfocusGrid"),
uiOutput("histFocusUIfocusX")
)
withLoader(plotOutput("histFocus", height = 700)),
uiOutput("histFocusUI")
),
tabPanel("Heatmap",
withLoader(plotOutput("Heatmap", height = 700)),
......@@ -181,12 +173,12 @@ shinyUI(dashboardPage(
Questions, problems or comments regarding this application should be sent to
<a href = \"mailto:cedric.midoux@irstea.fr?subject=[Easy16S]\">cedric.midoux@irstea.fr</a>
</p>
<p>
For more information about this tool, you can refer to
<a href = \"http://migale.jouy.inra.fr/sites/migale.jouy.inra.fr.drupal7.migale.jouy.inra.fr/files/JOBIM2018_poster.pdf\">this poster</a>.
</p>
<p>
<u>The demo dataset :</u> Chaillou, S., et al. \"
<a href = \"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4409155/\">
......
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