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Commit bca98b60 authored by Sebastien Theil's avatar Sebastien Theil
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Add colors and options.

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markdown/bars2.Rmd
+ 24
− 20
View file @ bca98b60
......@@ -26,17 +26,19 @@ if('bars' %in% names(rmd_data)){
```
```{r hold=TRUE, echo=FALSE, comment = FALSE, message= FALSE, warning = FALSE, results='asis', fig.keep='all', fig.align='left', fig.width = 20, fig.height = 10}
cat('## Phylum')
cat('\n')
rmd_data$bars[['Phylum']]
```
```{r hold=TRUE, echo=FALSE, comment = FALSE, message= FALSE, warning = FALSE, results='asis', fig.keep='all', fig.align='left', fig.width = 20, fig.height = 10}
cat('\n')
cat('## Family')
cat('\n')
grid.draw(rmd_data$bars[['Family']])
```
```{r hold=TRUE, echo=FALSE, comment = FALSE, message= FALSE, warning = FALSE, results='asis', fig.keep='all', fig.align='left', fig.width = 20, fig.height = 10}
cat('## Genus')
cat('\n')
rmd_data$bars[['Genus']]
```
```{r hold=TRUE, echo=FALSE, comment = FALSE, message= FALSE, warning = FALSE, results='asis', fig.keep='all', fig.align='left', fig.width = 20, fig.height = 10}
cat('\n')
cat('## Genus')
cat('\n')
grid.draw(rmd_data$bars[['Genus']])
```
```{r hold=TRUE, echo=FALSE, comment = FALSE, message= FALSE, warning = FALSE, results='asis',fig.keep='all', fig.align='left', fig.width = 20, fig.height = 10}
if('compo' %in% names(rmd_data)){
......@@ -45,15 +47,17 @@ if('compo' %in% names(rmd_data)){
}
```
```{r hold=TRUE, echo=FALSE, comment = FALSE, message= FALSE, warning = FALSE, results='asis', fig.keep='all', fig.align='left', fig.width = 20, fig.height = 10}
cat('## Phylum')
cat('\n')
rmd_data$compo[['Phylum']]
```
```{r hold=TRUE, echo=FALSE, comment = FALSE, message= FALSE, warning = FALSE, results='asis', fig.keep='all', fig.align='left', fig.width = 20, fig.height = 10}
cat('\n')
cat('## Family')
cat('\n')
grid.draw(rmd_data$compo[['Family']])
```
```{r hold=TRUE, echo=FALSE, comment = FALSE, message= FALSE, warning = FALSE, results='asis', fig.keep='all', fig.align='left', fig.width = 20, fig.height = 10}
cat('## Genus')
cat('\n')
rmd_data$compo[['Genus']]
```
```{r hold=TRUE, echo=FALSE, comment = FALSE, message= FALSE, warning = FALSE, results='asis', fig.keep='all', fig.align='left', fig.width = 20, fig.height = 10}
cat('\n')
cat('## Genus')
cat('\n')
grid.draw(rmd_data$compo[['Genus']])
```
\ No newline at end of file
plot_stats/bars.R
+ 34
− 20
View file @ bca98b60
......@@ -13,10 +13,14 @@ option_list = list(
help="output .Rdata file name for plot_bar. [default= %default]", metavar="path"),
make_option(c("-a", "--column1"), type="character", default="",
help="Column name. [default= %default]", metavar="STR"),
make_option(c("-b", "--column2"), type="character", default="",
help="Column name. [default= %default]", metavar="STR"),
make_option(c("-s", "--sname"), type="logical", default=FALSE,
help="Change sample.id by they factor in graph. [default= %default]", metavar="STR"),
make_option(c("-n", "--num"), type="integer", default=10,
help="Number of top taxon to display. [default= %default]", metavar="STR"),
make_option(c("-e", "--rare"), type="character", default=NULL,
help="Column name for rare curves. [default= %default]", metavar="STR"),
make_option(c("-b", "--column2"), type="character", default="",
help="Column name. [default= %default]", metavar="STR"),
make_option(c("-i", "--rank"), type="character", default="Genus",
help="Taxonomic rank name. You can provide multiple ranks seperate by comma.[default= %default]", metavar="STR")
);
......@@ -59,6 +63,7 @@ suppressMessages(library('ggplot2'))
suppressMessages(library('gridExtra'))
suppressMessages(library('grid'))
suppressMessages(library('microbiome'))
suppressMessages(library('viridis'))
suppressMessages(source("https://raw.githubusercontent.com/mahendra-mariadassou/phyloseq-extended/master/load-extra-functions.R"))
suppressMessages(library(plotly))
load(opt$rdata)
......@@ -78,12 +83,17 @@ if(opt$bar==TRUE){
for(i in 1:length(taxonomy)){
j <- taxonomy[i]; print(j)
psobj.top10 <- microbiome::aggregate_top_taxa(data, j, top = 10)
psobj.top <- microbiome::aggregate_top_taxa(data, j, top = opt$num)
if(opt$column1 != '' & opt$column2 == ''){
flog.info('Plotting bar (%s)...',j)
plot.composition.COuntAbun <- microbiome::plot_composition(psobj.top10, x.label = "sample.id",
sample.sort=opt$column1) + theme(legend.position = "bottom") +
scale_fill_brewer(j, palette = "Paired") + theme_bw() +
if(opt$sname == TRUE){
plot.composition.COuntAbun <- microbiome::plot_composition(psobj.top, x.label = opt$column1, sample.sort=opt$column1)
} else{
plot.composition.COuntAbun <- microbiome::plot_composition(psobj.top, x.label = "sample.id", sample.sort=opt$column1)
}
plot.composition.COuntAbun <- plot.composition.COuntAbun + theme(legend.position = "bottom") +
theme_bw() + scale_fill_viridis(discrete = TRUE) +
theme(axis.text.x = element_text(angle = 90)) +
ggtitle("Raw abundance") + theme(legend.title = element_text(size = 18))
......@@ -93,17 +103,23 @@ if(opt$bar==TRUE){
else if(opt$column1 != '' & opt$column2 != ''){
flog.info('Plotting bar (%s)...',j)
sdata = psobj.top10@sam_data@.Data
names(sdata) = psobj.top10@sam_data@names
sdata = psobj.top@sam_data@.Data
names(sdata) = psobj.top@sam_data@names
FACT1=sdata[[opt$column2]]
lvls = levels(sdata[[opt$column2]])
LL <- list()
for(i in 1:length(lvls)){
fun <- paste("ppp <- subset_samples(psobj.top10, ",opt$column2," %in% '",lvls[i],"')",sep="")
fun <- paste("ppp <- subset_samples(psobj.top, ",opt$column2," %in% '",lvls[i],"')",sep="")
eval(parse(text=fun))
p1 <- microbiome::plot_composition(ppp, x.label = "sample.id",
verbose=TRUE,sample.sort=opt$column1) + theme(legend.position = "bottom") +
scale_fill_brewer(j, palette = "Paired") + theme_bw() +
if(opt$sname){
p1 <- microbiome::plot_composition(ppp, x.label = opt$column1, verbose=TRUE,sample.sort=opt$column1)
} else{
p1 <- microbiome::plot_composition(ppp, x.label = "sample.id", verbose=TRUE,sample.sort=opt$column1)
}
p1 <- p1 + theme(legend.position = "bottom") +
theme_bw() + scale_fill_viridis(discrete = TRUE) +
theme(axis.text.x = element_text(angle = 90), legend.title = element_text(size = 18)) +
ggtitle(paste("Raw abundance",opt$column2,"=", lvls[i]))
......@@ -117,8 +133,6 @@ if(opt$bar==TRUE){
leg = ggpubr::get_legend(p1)
LL[[i+1]] <- ggpubr::as_ggplot(leg)
}
}
plot.composition.COuntAbun <- p3 <- gridExtra::grid.arrange(grobs=LL, ncol=length(lvls)+1)
......@@ -149,10 +163,10 @@ compo <- function (rankList, psobj, var = 'sample.id', col2='') {
fun <- paste("ppp <- subset_samples(psobj, ",opt$column2," %in% '",LVL,"')",sep="")
eval(parse(text=fun))
flog.info('Plotting %s composition (%s)...',var, j)
psobj.fam <- microbiome::aggregate_top_taxa(ppp, j, top = 10)
psobj.fam <- microbiome::aggregate_top_taxa(ppp, j, top = opt$num)
psobj.rel <- microbiome::transform(psobj.fam, "compositional")
p1 <- microbiome::plot_composition(psobj.rel, x.label = "sample.id", sample.sort=opt$column1) +
theme() + scale_fill_brewer(j, palette = "Paired") + theme_bw() +
p1 <- microbiome::plot_composition(psobj.rel, x.label = opt$column1, sample.sort=opt$column1) +
theme() + theme_bw() + scale_fill_viridis(discrete = TRUE) +
theme(axis.text.x = element_text(angle = 90), legend.title = element_text(size = 18)) +
ggtitle(paste("Raw abundance",opt$column2,"=", LVL))
......@@ -182,10 +196,10 @@ compo <- function (rankList, psobj, var = 'sample.id', col2='') {
for(i in 1:length(rankList)){
j <- rankList[i]
flog.info('Plotting %s composition (%s)...',var, j)
psobj.fam <- microbiome::aggregate_top_taxa(psobj, j, top = 10)
psobj.fam <- microbiome::aggregate_top_taxa(psobj, j, top = opt$num)
psobj.rel <- microbiome::transform(psobj.fam, "compositional")
p1 <- microbiome::plot_composition(psobj.rel, x.label = "sample.id", sample.sort=opt$column1) +
theme() + scale_fill_brewer(j, palette = "Paired") + theme_bw() +
p1 <- microbiome::plot_composition(psobj.rel, x.label = opt$column1, sample.sort=opt$column1) +
theme() + theme_bw() + scale_fill_viridis(discrete = TRUE) +
theme(axis.text.x = element_text(angle = 90), legend.title = element_text(size = 18)) +
ggtitle("Relative abundance")
fun <- paste('rmd_data$compo$',j,' <- p1',sep='')
......
plot_stats/diversity_beta.R
+ 1
− 1
View file @ bca98b60
library(futile.logger)
suppressMessages(library("optparse"))
suppressMessages(library("optparse"))
options(warn=-1)
option_list = list(
......
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