The qa() function of the ShortRead bioconductor library generates quality statistics from fastq files. The report() function then prepares a report of the various measures in an html format. A few other questions on this site have recommended using the display_html() function of IRdisplay to show html in jupyter notebooks using R (irkernel). However it only throws errors for me when trying to display an html report generated by the report() function of ShortRead.
library("ShortRead")
sample_dir <- system.file(package="ShortRead", "extdata", "E-MTAB-1147") # A sample fastq file
qa_object <- qa(sample_dir, "*fastq.gz$")
qa_report <- report(qa_object, dest="test") # Makes a "test" directory containing 'image/', 'index.html' and 'QA.css'
library("IRdisplay")
display_html(file = "test/index.html")
Gives me:
Error in read(file, size): unused argument (size)
Traceback:
1. display_html(file = "test/index.html")
2. display_raw("text/html", FALSE, data, file, isolate_full_html(list(`text/html` = data)))
3. prepare_content(isbinary, data, file)
4. read_all(file, isbinary)
Is there another way to display this report in jupyter with R?
It looks like there's a bug in the code. The quick fix is to clone the github repo, and make the following edit to the ./IRdisplay/R/utils.r, and on line 38 change the line from:
read(file,size)
to
read(size)
save the file, switch to the parent directory, and create a new tarbal, e.g.
tar -zcf IRdisplay.tgz IRdisplay/
and then re-install your new version, e.g. after re-starting R, type:
install.packages( "IRdisplay.tgz", repo=NULL )
Related
I am extracting prosody features from an audio file while using Opensmile using Windows version of Opensmile. It runs successful and an output csv is generated. But when I open csv, it shows some rows that are not readable. I used this command to extract prosody feature:
SMILEXtract -C \opensmile-3.0-win-x64\config\prosody\prosodyShs.conf -I audio_sample_01.wav -O prosody_sample1.csv
And the output of csv looks like this:
[
Even I tried to use the sample wave file given in Example audio folder given in opensmile directory and the output is same (not readable). Can someone help me in identifying where the problem is actually? and how can I fix it?
You need to enable the csvSink component in the configuration file to make it work. The file config\prosody\prosodyShs.conf that you are using does not have this component defined and always writes binary output.
You can verify that it is the standart binary output in this way: omit the -O parameter from your command so it becomesSMILEXtract -C \opensmile-3.0-win-x64\config\prosody\prosodyShs.conf -I audio_sample_01.wav and execute it. You will get a output.htk file which is exactly the same as the prosody_sample1.csv.
How output csv? You can take a look at the example configuration in opensmile-3.0-win-x64\config\demo\demo1_energy.conf where a csvSink component is defined.
You can find more information in the official documentation:
Get started page of the openSMILE documentation
The section on configuration files
Documentation for cCsvSink
This is how I solved the issue. First I added the csvSink component to the list of the component instances. instance[csvSink].type = cCsvSink
Next I added the configuration parameters for this instance.
[csvSink:cCsvSink]
reader.dmLevel = energy
filename = \cm[outputfile(O){output.csv}:file name of the output CSV
file]
delimChar = ;
append = 0
timestamp = 1
number = 1
printHeader = 1
\{../shared/standard_data_output_lldonly.conf.inc}`
Now if you run this file it will throw you errors because reader.dmLevel = energy is dependent on waveframes. So the final changes would be:
[energy:cEnergy]
reader.dmLevel = waveframes
writer.dmLevel = energy
[int:cIntensity]
reader.dmLevel = waveframes
[framer:cFramer]
reader.dmLevel=wave
writer.dmLevel=waveframes
Further reference on how to configure opensmile configuration files can be found here
I wrote an HTML vignette for my R package hosted on GitHub. When I open it with browseVignettes, it flawlessly opens on the browsers showing this content:
Vignettes found by browseVignettes("package_name")
Vignettes in package package_name
package_name file_name - HTML source R code
clicking on HTML source R code it opens the same file in three different versions.
However, I don't need the source and the R code files to show.
Is there a way to output only the HTML file? As in the following output
Vignettes found by browseVignettes("package_name")
Vignettes in package package_name
package_name file_name - HTML
You can't easily drop the source, but you can drop the R code by setting that component to blank. For example,
allfields <- browseVignettes()
noR <- lapply(allfields, function(pkg) {pkg[,"R"] <- ""; pkg})
class(noR) <- class(allfields)
noR
If you really want to drop the source, then you'll need to get the print method and modify it:
print.browseVignettes <- utils:::print.browseVignettes
# Modify it as you like.
I am running a knime chunk loop to write always the same procedure in different csv files:
The Part with the python script until the csv write is working, when I do it without loop, but somehow he is not writing in the customized folder path, if I have the loop inside.
The target is to write a new csv-file for every loop (the output is a list).
The nodes are:
Chunk Loop: Rows per chunk: 51
Create file name:
Options Selected directioy: C:/....
Flow Variables: FileName: currentIteration
CSV Writer: Flow Variables: filename: CurrentIteration
How can I change the folder path of the file? He is always saving it in the default folder
Here is an example workflow (apologies for the weird blurry Windows 10 screenshots):
Create File Name config:
CSV Writer config:
You may need to run each node individually in order to create the flow variable before you can select it in the following node.
I have a FlexTable produced with the ReporteRs package which I would like to export as .html.
When I print the table to the viewer in RStudio I can do this by clicking on 'Export' and selecting 'Save as webpage'.
How would I replicate this action in my script?
I don't want to knit to a html document or produce a report just yet as at present I just want separate files for each of my draft tables which I can share with collaborators (but nicely formatted so they are easy to read).
I have tried the as.html function and that does produce a .html file but all the formatting is missing (it is just plain text).
Here is a MWE:
# load libraries:
library(data.table)
library(ReporteRs)
library(rtable)
# Create dummy table:
mydt <- data.table(id = c(1,2,3), name = c("a", "b", "c"), fruit = c("apple", "orange", "banana"))
# Convert to FlexTable:
myflex <- vanilla.table(mydt)
# Attempt to export to html in script:
sink('MyFlexTable.html')
print(as.html(myflex))
sink()
# Alternately:
sink('MyFlexTable.html')
knit_print(myflex)
sink()
The problem with both methods demonstrated above is that they output the table without any formatting (no borders etc).
However, manually selecting 'export' and 'save as webpage' in RStudio renders the FlexTable to a html file with full formatting. Why is this?
This works for me:
writeLines(as.html(myflex), "MyFlexTable.html")
I run an application that generates and updates a number of files in a specific folder. While the application runs, I observe the content of the folder through the sublime sidebar. Because I am interested to see the current size of each file while the application runs, I have an open terminal (Mac) where I use the following command to get the live state of the folder.
watch -d ls -al -h folderName
I was wondering if I can obtain this information directly from sublime.
So my question is: Is it possible to have the size of each file next to the file-names in the sublime sidebar? And if yes, how?
Since the sidebar is not in the official API, I don't think this is possible or at least it is not easy.
However getting the information into sublime text is easy. You can archive this by using a view. Just execute the ls command and write the result in the view.
I wrote a small (ST3) plugin for this purpose:
import subprocess
import sublime
import sublime_plugin
# change to whatever command you want to execute
commands = ["ls", "-a", "-s", "-1", "-h"]
# the update interval
TIMEOUT = 2000 # ms
def watch_folder(view, watch_command):
"""create a closure to watch a folder and update the view content"""
window = view.window()
def watch():
# stop if the view is not longer open
open_views = [v.id() for v in window.views()]
if view.id() not in open_views:
print("closed")
return
# execute the command and read the output
output = subprocess.check_output(watch_command).decode()
# replace the view content with the output
view.set_read_only(False)
view.run_command("select_all")
view.run_command("insert", {"characters": output})
view.set_read_only(True)
# call this function again after the interval
sublime.set_timeout(watch, TIMEOUT)
return watch
class WatchFolderCommand(sublime_plugin.WindowCommand):
def run(self):
folders = self.window.folders()
if not folders:
sublime.error_message("You don't have opened any folders")
return
folder = folders[0] # get the first folder
watch_command = commands + [folder]
# create a view and set the desired properties
view = self.window.new_file()
view.set_name("Watch files")
view.set_scratch(True)
view.set_read_only(True)
view.settings().set("auto_indent", False)
# create and call the watch closure
watch_folder(view, watch_command)()
Just open the User folder (or any other sub-folder of Packages), create a python file (e.g. watch_folder.py) and paste the source code.
You can bind it to a keybinding by pasting the following to your keymap:
{
"keys": ["ctrl+alt+shift+w"],
"command": "watch_folder",
},