Plot error with plotting string values

Question

Oganes Khatchikian 2023-12-16

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此问题的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/2061227-plot-error-with-plotting-string-values

评论： Stephen23 2023-12-27

在 MATLAB Online 中打开

Code is executing correctly but would like to have the original and the mutated strings on the plot

% Simulate DNA sequence evolution with mutations

sequenceLength = 50;

mutationRate = 0.02;

% Generate random DNA sequence

originalSequence = randsample(['A', 'T', 'C', 'G'], sequenceLength, true);

% Introduce mutations

mutatedSequence = originalSequence;

mutationPositions = rand(1, sequenceLength) < mutationRate;

mutatedSequence(mutationPositions) = randsample(setdiff(['A', 'T', 'C', 'G'], mutatedSequence(mutationPositions)), sum(mutationPositions), true);

% Display original and mutated sequences

disp('Original Sequence:');

Original Sequence:

disp(originalSequence);

TGGGTAGCCCGATTTATTGCCAATGATTTGACCCGCCAGCCAGGGTGCGA

disp('Mutated Sequence:');

Mutated Sequence:

disp(mutatedSequence);

TGGGTAGCCCGATTTATTGCCAATGATTTGACCCGCCAGCCAGTGTGCGA

% Bayesian Inference to detect mutations

priorProbabilityMutation = 0.01; % Prior probability of mutation

likelihoodMutation = mutationRate; % Likelihood of observing a mutation

% Bayes' Theorem for each position

posteriorProbabilityMutation = zeros(1, sequenceLength);

for i = 1:sequenceLength

evidence = strcmp(originalSequence(i), mutatedSequence(i));

posteriorProbabilityMutation(i) = (likelihoodMutation * priorProbabilityMutation) / ((likelihoodMutation * priorProbabilityMutation) + (~evidence * (1 - priorProbabilityMutation)));

end

% Set a threshold for detecting mutations

threshold = 0.5;

detectedMutations = posteriorProbabilityMutation > threshold;

% Display results

disp('Posterior Probability of Mutation:');

Posterior Probability of Mutation:

disp(posteriorProbabilityMutation);

Columns 1 through 19 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 Columns 20 through 38 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000 Columns 39 through 50 1.0000 1.0000 1.0000 1.0000 1.0000 0.0002 1.0000 1.0000 1.0000 1.0000 1.0000 1.0000

disp('Detected Mutations:');

Detected Mutations:

disp(detectedMutations);

Columns 1 through 49 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 Column 50 1

% Visualization

figure;

subplot(3, 1, 1);

bar(posteriorProbabilityMutation, 'b');

xlabel('Position');

ylabel('Posterior Probability of Mutation');

title('Bayesian Inference');

grid on;

subplot(3, 1, 2);

plot(originalSequence, 'bo', 'LineWidth', 2);

Error using plot
Invalid first data argument.

hold on;

plot(mutatedSequence, 'rx', 'LineWidth', 2);

scatter(find(detectedMutations), ones(1, sum(detectedMutations)), 'g', 'filled');

legend('Original Sequence', 'Mutated Sequence', 'Detected Mutations');

xlabel('Position');

ylabel('Nucleotide');

title('DNA Sequence and Mutations');

grid on;

hold off;

subplot(3, 1, 3);

stem(detectedMutations, 'r', 'LineWidth', 2);

xlabel('Position');

ylabel('Mutation Detected');

title('Mutation Detection');

grid on;

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Walter Roberson 2023-12-16

See text

Stephen23 2023-12-17

Or if you want that text as tick marks along the axes, then you could use:

https://www.mathworks.com/help/matlab/categorical-arrays.html

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Answer 1

SAI SRUJAN 2023-12-27

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链接

此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/2061227-plot-error-with-plotting-string-values#answer_1378372

在 MATLAB Online 中打开

Hi Oganes,

I understand that you are facing an issue with displaying both the original and mutated DNA sequences on a plot.

An error is encountered with the 'plot' function as the character arrays representing DNA sequences are being passed, whereas the 'plot' function expects numerical inputs. To render the DNA sequences graphically via the 'plot' function, each nucleotide can be mapped to a distinct numerical value, followed by plotting the corresponding numbers.

Follow the given code snippet to proceed further,

% Convert sequences to numerical arrays for plotting
originalSequenceNum = nucleotideToNumber('AGGGTGCGA');
mutatedSequenceNum = nucleotideToNumber('AGTGTGCGA');
plot(originalSequenceNum);
hold on;
plot(mutatedSequenceNum);
legend('Original Sequence', 'Mutated Sequence');
xlabel('Position');
ylabel('Nucleotide');
title('DNA Sequence and Mutations');
set(gca, 'ytick', 1:4, 'yticklabel', {'A', 'T', 'C', 'G'});
% A mapping function for the nucleotides to numerical values:
function numArray = nucleotideToNumber(s)
    map = containers.Map({'A', 'T', 'C', 'G'}, 1:4);
    numArray = zeros(size(s));
    for i = 1:length(s)
        numArray(i) = map(s(i));
    end
end

For a comprehensive understanding of the 'plot' function in MATLAB, please refer to the following documentation.

https://www.mathworks.com/help/matlab/ref/plot.html

I hope it helps.

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Stephen23 2023-12-27

在 MATLAB Online 中打开

A simpler approach is to use CATEGORICAL arrays (which PLOT also accepts, it even labels the tickmarks correctly using the categories):

S = ["A","T","C","G"];

originalSequenceNum = categorical(num2cell('AGGGTGCGA'),S)

originalSequenceNum = 1×9 categorical array

A G G G T G C G A

mutatedSequenceNum = categorical(num2cell('AGTGTGCGA'),S)

mutatedSequenceNum = 1×9 categorical array

A G T G T G C G A

plot(originalSequenceNum);

hold on;

plot(mutatedSequenceNum);

legend('Original Sequence', 'Mutated Sequence');

xlabel('Position');

ylabel('Nucleotide');

title('DNA Sequence and Mutations');

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Plot error with plotting string values

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Plot error with plotting string values

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