I want do find and replace all in matlab (As we do in MS office).
https://www.dropbox.com/s/hxfqunjwhnvkl1f/matlab.mat?dl=0
I have a cell array LUT_HS_complete (contains identifier in column 1 and protein name in column 2 and summary in column 3) this is my look up table. on the other hand, I have my protein-protein interaction data (named Second_layer with identifiers in first two columns and the score in column 3).
I want to replace the first two columns in my Second_layer with the corresponding protein name from my look up table.
I tried strmatch, but that didn't help me.
Source_gene = Second_layer(:,1); Source_gene = regexprep(Source_gene,'[-/\s]','');
Target_gene = Second_layer(:,2); Target_gene = regexprep(Target_gene,'[-/\s]','');
Inter_score = Second_layer(:,3);
%%
for i=1:length(Source_gene(1:end,1));
SG = strmatch(Source_gene(i),LUT_HS_complete(1:end,1),'exact');
renamed_Source_gene(SG,1) = LUT_HS_complete(SG,2);
end
for j=1:length(Target_gene(1:end,1));
TG = strmatch(Target_gene(j),LUT_HS_complete(1:end,1),'exact');
renamed_Target_gene(TG,1) = LUT_HS_complete(TG,2);
end
If you could find a solution. It would be a great help.
Might this work for you?
renamed_Second_layer(:,1)=LUT_HS_complete(cellfun(#(x) find(strcmp(x,LUT_HS_complete(:,1))),Second_layer(:,1)),2);
renamed_Second_layer(:,2)=LUT_HS_complete(cellfun(#(x) find(strcmp(x,LUT_HS_complete(:,1))),Second_layer(:,2)),2);
renamed_Second_layer(:,3)=Second_layer(:,3);
Related
I have a problem I hope you can help me with.
I have imported a large dataset (200000 x 5 cell) in Matlab that has the following structure:
'Year' 'Country' 'X' 'Y' 'Value'
Columns 1 and 5 contain numeric values, while columns 2 to 4 contain strings.
I would like to arrange all this information into a variable that would have the following structure:
NewVariable{Country_1 : Country_n , Year_1 : Year_n}(Y_1 : Y_n , X_1 : X_n)
All I can think of is to loop through the whole dataset to find matches between the names of the Country, Year, X and Y variables combining the if and strcmp functions, but this seems to be the most ineffective way of achieving what I am trying to do.
Can anyone help me out?
Thanks in advance.
As mentioned in the comments you can use categorical array:
% some arbitrary data:
country = repmat('ca',10,1);
country = [country; repmat('cb',10,1)];
country = [country; repmat('cc',10,1)];
T = table(repmat((2001:2005)',6,1),cellstr(country),...
cellstr(repmat(['x1'; 'x2'; 'x3'],10,1)),...
cellstr(repmat(['y1'; 'y2'; 'y3'],10,1)),...
randperm(30)','VariableNames',{'Year','Country','X','Y','Value'});
% convert all non-number data to categorical arrays:
T.Country = categorical(T.Country);
T.X = categorical(T.X);
T.Y = categorical(T.Y);
% here is an example for using categorical array:
newVar = T(T.Country=='cb' & T.Year==2004,:);
The table class is made for such things, and very convenient. Just expand the logic statement in the last line T.Country=='cb' & T.Year==2004 to match your needs.
Tell me if this helps ;)
I am beginning to use torch 7 and I want to make my dataset for classification. I've already made pixel images and corresponding labels. However, I do not know how to feed those data to the torch. I read some codes from others and found out that they are using the dataset whose extension is '.t7' and I think it is a tensor type. Is it right? And I wonder how I can convert my pixel images(actually, I made them with Matlab by using MNIST dataset) into t7 extension compatible to the torch. There must be structure of dataset in the t7 format but I cannot find it (also for the labels too).
To sum up, I have pixel images and labels and want to convert those to t7 format compatible to the torch.
Thanks in advance!
The datasets '.t7' are tables of labeled Tensors.
For example the following lua code :
if (not paths.filep("cifar10torchsmall.zip")) then
os.execute('wget -c https://s3.amazonaws.com/torch7/data/cifar10torchsmall.zip')
os.execute('unzip cifar10torchsmall.zip')
end
Readed_t7 = torch.load('cifar10-train.t7')
print(Readed_t7)
Will return through itorch :
{
data : ByteTensor - size: 10000x3x32x32
label : ByteTensor - size: 10000
}
Which means the file contains a table of two ByteTensor one labeled "data" and the other one labeled "label".
To answer your question, you should first read your images (with torchx for example : https://github.com/nicholas-leonard/torchx/blob/master/README.md ) then put them in a table with your Tensor of label. The following code is just a draft to help you out. It considers the case where : there are two classes, all your images are in the same folder and are ordered through those classes.
require 'torchx';
--Read all your dataset (the chosen extension is png)
files = paths.indexdir("/Path/to/your/images/", 'png', true)
data1 = {}
for i=1,files:size() do
local img1 = image.load(files:filename(i),3)
table.insert(data1, img1)
end
--Create the table of label according to
label1 = {}
for i=1, #data1 do
if i <= number_of_images_of_the_first_class then
label1[i] = 1
else
label1[i] = 2
end
end
--Reshape the tables to Tensors
label = torch.Tensor(label1)
data = torch.Tensor(#data1,3,16,16)
for i=1, #data1 do
data[i] = data1[i]
end
--Create the table to save
Data_to_Write = { data = data, label = label }
--Save the table in the /tmp
torch.save("/tmp/Saved_Data.t7", Data_to_Write)
It should be possible to make a less hideous code but this one details all the steps and works with torch 7 and Jupyter 5.0.0 .
Hope it helps.
Regards
I have created a structure about patient. Its fields are name, age, etc. I want to be able to retrieve a patient's all info by entering its name or any other unique property. In other words, how can I find the patient's index? Thanks in advance.
patient(10).name = 'Chuck';
patient(10).age = 29;
patient(11).name = 'Sarah';
patient(11).name = 28;
Structures are not a good data type for doing what you want.
I suggest using a table. If you have your data in the structure already, call
patientTable = struct2table(patient);
Then, you get the index as:
chucksIndex = find( strcmp( patientTable.name, 'Chuck'))
And you get that patient's information as
patientTable(chucksIndex,:)
(note: if all you need the index for is lookup, you don't need to call find, the logical index from strcmp suffices).
Double-clicking the table in the workspace browser presents the data in an Excel-like fashion. The only thing you'll have to change in your code is accessing the data. Instead of
patient(10).name
patient(10).age
You write
patientTable.name{10}
patientTable.age(10)
If you do not want to use a table, you can get the index as:
chucksIndex = find(strcmp({patient.name},'Chuck'));
First, there is an error, it should be patient(11).name = 28;.
Here is a way this should work. I've started the indexes for Chuck and Sarah at 1.
patient(1).name = 'Chuck';
patient(1).age = 29;
patient(2).name = 'Sarah';
patient(2).age = 28;
% Assign to cell array
plist = {patient.name};
% Choose the name of a patient
choose_patient = 'Sarah';
% Find the chosen patient in the list
ix_patient = find(strcmp(plist, choose_patient))
% Get full entry for that patient
patient(ix_patient)
In MatLab, I have several data vectors that are in text. For example:
speciesname = [species1 species2 species3];
genomelength = [8 10 5];
gonometype = [RNA DNA RNA];
I realise that to make a plot, arrays must be numerical. Is there a quick and easy way to assign unique entries in an array a number, for example so that RNA = 1 and DNA = 2? Note that some arrays might not be binary (i.e. have more than two options).
Thanks!
So there is a quick way to do it, but im not sure that your plots will be very intelligible if you use numbers instead of words.
You can make a unique array like this:
u = unique(gonometype);
and make a corresponding number array is just 1:length(u)
then when you go through your data the number of the current word will be:
find(u == current_name);
For your particular case you will need to utilize cells:
gonometype = {'RNA', 'DNA', 'RNA'};
u = unique(gonometype)
u =
'DNA' 'RNA'
current = 'RNA';
find(strcmp(u, current))
ans =
2
I need to load a data file, test.dat, into Matlab. The contents of data file are like
*a682 1233~0.2
*a2345 233~0.8 345~0.2 4567~0.3
*a3457 345~0.9 34557~1.2 34578~0.2 9809~0.1 2345~2.9 23452~0.9 334557~1.2 234578~0.2 19809~0.1 23452~2.9 3452~0.9 4557~1.2 3578~0.2 92809~0.1 12345~2.9 232452~0.9 33557~1.6 23478~0.6 198099~2.1 234532~2.9 …
How to read this type of file into matlab, and use the terms, such as *2345 to identify a row, which links to corresponding terms, including 233~0.8 345~0.2 4567~0.3
Thanks.
Because each of the rows is a different size, you either have to make a cell array, a structure, or deal with adding NaN or zero to a matrix. I chose to use a cell array, hope it is ok! If someone is better with regexp than me please comment, the output cells are now not perfect (i.e. show 345~ instead of 345~0.9) but I am sure it is a minor fix. Here is the code:
datfile = 'test.dat';
text = fileread(datfile);
row1 = regexp(text,'*[a-z]?\d+','match');
data(:,1) = row1';
row2 = regexp(text,'*[a-z]?\d+','split');
row2 = [row2(:,2:end)'];
for i = 1:size(row2,1)
data{i,2} = regexp(row2{i},'\d+\S\d+\s','split');
end
What this creates is a cell array called data where the first column of every row is your *a682 id and the second column of each row is a cell with your data values. To get them you could use:
data{1}
to show the id
data{1,2}
to show the cell contents
data{1,2}{1}
to show the specific data point
This should work and is relatively simple!