I am testing a script to delete unwanted directories with Robocopy:
#echo off
set maxdepth=3
set source=.
robocopy %source% %source% /s /purge /lev:%maxdepth% /xd unwantedDirectory
However, the directories remain untouched.
I have tried EnableDelayedExpansion with the % changed to ! but still no joy. I have tried replacing option /s with /e for empty directories & replacing /purge with /mir but still, they do not delete.
The terminal printout shows no unwantedDirectory in the directory tree:
Source : G:\
Dest : G:\
Files : *.*
Exc Dirs : unwantedDirectory
Options : *.* /S /DCOPY:DA /COPY:DAT /PURGE /LEV:3 /R:1000000 /W:30
3 G:\
0 G:\$RECYCLE.BIN\
0 G:\$RECYCLE.BIN\S-1-5-21-1628594993-1838746295-2145544969-1000\
3 G:\$RECYCLE.BIN\S-1-5-21-3144879857-1687253292-3729363637-1001\
0 G:\$RECYCLE.BIN\S-1-5-21-3144879857-1687253292-3729363637-1005\
0 G:\Backups_01\
1 G:\Backups_01\2022-02-15 1409\
1 G:\Backups_01\2022-07-17 1725\
1 G:\Backups_01\2022-10-22 1335\
1 G:\Backups_01\2022-11-20 1922\
1 G:\Backups_01\2022-12-18 1812\
0 G:\Backups_01\example\
29 G:\Backups_02\
0 G:\Recovery\
Total Copied Skipped Mismatch FAILED Extras
Dirs : 17 0 14 0 3 0
Files : 40 0 40 0 0 0
Bytes : 3.562 g 0 3.562 g 0 0 0
Times : 0:00:00 0:00:00 0:00:00 0:00:00
Goodmorning everyone, I have a data.ped file made up of thousands of columns and hundreds of lines. The first 6 columns and the first 4 lines of the file look like this:
186 A_Han-4.DG 0 0 1 1
187 A_Mbuti-5.DG 0 0 1 1
188 A_Karitiana-4.DG 0 0 1 1
191 A_French-4.DG 0 0 1 1
And I have a ids.txt file that looks like this:
186 Ignore_Han(discovery).DG
187 Ignore_Mbuti(discovery).DG
188 Ignore_Karitiana(discovery).DG
189 Ignore_Yoruba(discovery).DG
190 Ignore_Sardinian(discovery).DG
191 Ignore_French(discovery).DG
192 Dinka.DG
193 Dai.DG
What I need is to replace (in unix) the value in the first column of the data.ped file with the value in the second column of the ids.txt that is in the same line of the value that is going to be replaced from the data.ped file. For example, I want to replace the "186" value from the data.ped first column with the "Ignore_Han(discovery).DG" value from the ids.txt second column (and this because in the first column of the same line of this value there is "186") So the output.ped file must look like this:
Ignore_Han(discovery).DG A_Han-4.DG 0 0 1 1
Ignore_Mbuti(discovery).DG A_Mbuti-5.DG 0 0 1 1
Ignore_Karitiana(discovery).DG A_Karitiana-4.DG 0 0 1 1
Ignore_French(discovery).DG A_French-4.DG 0 0 1 1
The values of the first column of the data.ped file are a subset of the values present in the first column of the ids.txt file. So there is always match.
Edit:
I've tried with this:
awk 'NR==FNR{a[$1]=$2; next} $1 in a{$1=a[$1]; print}' ids.txt data.ped
but when I check the result with:
cut -f 1-6 -d " " output.ped
I get this strange output:
A_Han-4.DG 0 0 1 1y).DG
A_Mbuti-5.DG 0 0 1 1y).DG
A_Karitiana-4.DG 0 0 1 1y).DG
A_French-4.DG 0 0 1 1y).DG
while if I use this command:
cut -f 1-6 -d " " output.ped | less
I get this:
Ignore_Han(discovery).DG^M A_Han-4.DG 0 0 1 1
Ignore_Mbuti(discovery).DG^M A_Mbuti-5.DG 0 0 1 1
Ignore_Karitiana(discovery).DG^M A_Karitiana-4.DG 0 0 1 1
Ignore_French(discovery).DG^M A_French-4.DG 0 0 1 1
and I can't figure out why there is that ^M in every line.
awk 'NR==FNR{a[$1]=$2; next} $1 in a{$1=a[$1]} 1' ids.txt data.ped
output:
Ignore_Han(discovery).DG A_Han-4.DG 0 0 1 1
Ignore_Mbuti(discovery).DG A_Mbuti-5.DG 0 0 1 1
Ignore_Karitiana(discovery).DG A_Karitiana-4.DG 0 0 1 1
Ignore_French(discovery).DG A_French-4.DG 0 0 1 1
This is a classic awk task with various modifications according to your requirements. Here we replaced the first field of data.ped only if we have found its value in the ids.txt, else we print the line unchanged. If you would like to remove lines that don't match:
awk 'NR==FNR{a[$1]=$2; next} $1 in a{$1=a[$1]; print}' ids.txt data.ped
There is no need for the input files to be sorted and the order of the second file is preserved.
UPDATE:
If you have Ctrl-M characters in your inputs, remove them first with
cat file | tr -d '^M' > file.tmp && mv file.tmp file
for any file you use. In general, I suggest running dos2unix for any text files that could contain characters like ^M or \r, usually coming from dos/windows editing.
Use join command to join two files
join ids.txt data.ped > temp
You can use cut command to remove the first column like:
cut -d " " -f 2- temp > output.ped
I have generate a heatmap with pheatmap and for some reasons, I want that the rows appear in a predefined order.
I see in previous posts that the solution is to set the paramater cluster_row to FALSE, and to order the matrix in the order we want, like this in my case:
Otu0085 Otu0086 Otu0087 Otu0088 Otu0091
AB200 0 0 0 0 0
2 91 0 2 1 0
20CF360 0 1 0 1 0
19CF359 0 0 0 2 0
11VP12 0 0 0 0 155
11VP04 4 1 0 0 345
However, when I do:
pheatmap(shared,cluster_rows = F)
My rows are sorted alphabetically, like this:
10CF278a
11
11AA07
11CF278b
11VP03
11VP04
11VP05
11VP06
11VP08
11VP09
ANy suggestions would be welcome
Thank's by advance
I have been looking for a way of having a stacked bar plot in an upsetR graph.
I downloaded the movies data set (from here) and added a column having only two values "M" and "C".
Below, information on how I loaded the data and added the "x" column.
Edit:
m <- read.csv(system.file("extdata", "movies.csv", package = "UpSetR"),
header = T, sep = ";")
nrow(m)
[1] 3883
x<-c(rep("M", 3000), rep("C", 883))
m<-cbind(m, x)
unique(m$x)
[1] M C
This is the structure of the data frame:
str(m)
'data.frame': 3883 obs. of 22 variables:
$ Name : Factor w/ 3883 levels "$1,000,000 Duck (1971)",..: 3577 1858 1483 3718 1175 1559 3010 3548 3363 1420 ...
$ ReleaseDate: int 1995 1995 1995 1995 1995 1995 1995 1995 1995 1995 ...
$ Action : int 0 0 0 0 0 1 0 0 1 1 ...
$ Adventure : int 0 1 0 0 0 0 0 1 0 1 ...
$ Children : int 1 1 0 0 0 0 0 1 0 0 ...
$ Comedy : int 1 0 1 1 1 0 1 0 0 0 ...
$ Crime : int 0 0 0 0 0 1 0 0 0 0 ...
$ Documentary: int 0 0 0 0 0 0 0 0 0 0 ...
$ Drama : int 0 0 0 1 0 0 0 0 0 0 ...
$ Fantasy : int 0 1 0 0 0 0 0 0 0 0 ...
$ Noir : int 0 0 0 0 0 0 0 0 0 0 ...
$ Horror : int 0 0 0 0 0 0 0 0 0 0 ...
$ Musical : int 0 0 0 0 0 0 0 0 0 0 ...
$ Mystery : int 0 0 0 0 0 0 0 0 0 0 ...
$ Romance : int 0 0 1 0 0 0 1 0 0 0 ...
$ SciFi : int 0 0 0 0 0 0 0 0 0 0 ...
$ Thriller : int 0 0 0 0 0 1 0 0 0 1 ...
$ War : int 0 0 0 0 0 0 0 0 0 0 ...
$ Western : int 0 0 0 0 0 0 0 0 0 0 ...
$ AvgRating : num 4.15 3.2 3.02 2.73 3.01 3.88 3.41 3.01 2.66 3.54 ...
$ Watches : int 2077 701 478 170 296 940 458 68 102 888 ...
$ x : Factor w/ 2 levels "M","C": 1 1 1 1 1 1 1 1 1 1 ...
Now I tried to implement the stacked bar plot as follow:
upset(m,
queries = list(
list(query = elements,
params = list("x", "M"), color = "#e69f00", active = T),
list(query = elements,
params = list("x", "C"), color = "#cc79a7", active = T)))
The result looks like this:
As you can see the proportions are wrong as there should be in each bar only two colors (factor) either "M" or "C".
This issue seems to be not a trivial one, as also pointed out here.
Does anyone have an idea on how to implement this in UpsetR?
Thanks a lot
Here is a way to create an upset plot with stacked barplot, but using my ComplexUpset rather than UpSetR:
library(ComplexUpset)
movies = as.data.frame(ggplot2movies::movies)
genres = colnames(movies)[18:24]
# for simplicity of examples, only use the complete data points
movies[movies$mpaa == '', 'mpaa'] = NA
movies = na.omit(movies)
upset(
movies,
genres,
base_annotations=list(
'Intersection size'=intersection_size(
counts=FALSE,
mapping=aes(fill=mpaa)
)
),
width_ratio=0.1
)
Please see more examples in the documentation.
The Installation instructions are available on GitHub: krassowski/complex-upset (there is also a comparison to UpSetR and other packages).
I had a similar problem and found this workaround:
library("UpSetR")
m <- read.csv(system.file("extdata", "movies.csv", package = "UpSetR"),
header = T, sep = ";")
x<-c(rep("M", 2000), rep("Q", 1000), rep("C", 883))
m<-cbind(m, x)
upset(m,
queries = list(
list(query = elements,
params = list("x", c("M","Q", "C")), color = "#e69f00", active = T),
list(query = elements,
params = list("x", c("Q","C")), color = "#cc79a7", active = T),
list(query = elements,
params = list("x", "C"), color = grey(0.7), active = T)))
The problem in the original example is that every query overlays over the total bar separately and starts at y=0. Thus, the remaining black part of the bar always has the exact same height as the purple part at the bottom. The workaround is to systematically add queries of combinations of the different values the variable can take:
Start with a query and a respective color for the combination of all possible values (here c("M","Q","C") as the second parameter to params = list()).
Successively leave out one of the possible values (e.g. c("Q","C") in the first step here). The value left out will be represented by the color of the query, the last one that still included it ("M" in this example).
Continue adding queries until you have only one value left for the second parameter to params = list().
It should be possible do this programmatically for larger numbers of possible values and providing some color palette. But this remains a workaround and a native implementation of stacking the queries would be nice to have--so if you would like to see this functionality, you might consider bumping up the respective issue over at the Github repo.
Below the nice answer by #dlaehnemann but a little bit modified in order to create that list of list using a loop as well as linking wanted colors to it.
m <- read.csv(system.file("extdata", "movies.csv", package = "UpSetR"), header = T, sep = ";")
x<-c(rep("M", 2000), rep("Q", 1000), rep("C", 883))
m<-cbind(m, x)
i<-0
mylist<-list()
vectorUniqueValue <- unique(m$x)
colors = colorRampPalette(c("#332288",'#fdff00','#FF0000',"#CC6677","#88CCEE",'#36870c','#b786d2','#7c3c06',"#DDCC77",'#192194','#52cff4','#4f9c8b',"#4477AA",'#808080'))(length(vectorUniqueValue))
while ( length(vectorUniqueValue)>0 ){
i<-i+1
mylist[[i]]<-list(query = elements, params = list("x",as.character(vectorUniqueValue)), color = colors[i], active = T)
vectorUniqueValue<-vectorUniqueValue[-1]
}
upset(m, queries = mylist)
Hope it helps a bit until maybe one day someone works on the issue on github !
I have a input uff file with 'n' no.of channels. I want to read the UFF file and also split the values based on each individual channel. Then store the result for each channel in separate file. Each channel always start with '-1' '58' etc., and end with '-1'.
Example channel_01 from the input UFF file:
-1
58
filename
22-Mar-2016 10:16:53
164
MnBrgFr-AC225R/N;50.9683995923 mV/m/s2
0 0 0 0 channel_01 0 0 NONE 0 0
2 1048576 1 0.00000E+00 8.19669930804e-06 0.00000E+00
17 0 0 0 Time s
1 0 0 0 MnBrgFr-AC225R/N m/s2
0 0 0 0 NONE NONE
0 0 0 0 NONE NONE
392.665124452 392.659048025 392.658404832 392.661676933 392.665882251 392.671989083
392.67634175 392.673743248 392.672398388 392.669360175 392.665533757 392.66088639
392.660390546 392.660975268 392.663400693 392.662668621 392.661209156 392.65498538
392.649463269 392.649580214 392.649259786 392.658580248 392.664715147 392.667051694
-1