Matlab-genomics is a collection of Matlab scripts to perform genomics analysis especially single-cell analysis.
These scripts were developed for He and Williams et al. 2020 Nature
The codes and resources related to the paper are here.
Single-cell analysis has been dominated by packages on open-source platforms such as R and python. However, Matlab has its own advantages and consistency. It saves users efforts trying to figure out package inter-compatibility and dependency. It has also been a first choice among many researchers originally in Physics and Neuroscience fields who are seeking to dive into the modern Bioinformatics realm. Therefore, I've assembled a set of handy scripts, some of which are borrowed from other repositories from GitHub and MathWork Fileexhange, if not created on my own, to accelerate Matlab fans' adaption to the Bioinformatics field.
Download the whole folder, and then point MATLAB to this folder as one of customer scripts. This is the code for Mac Users:
addpath(genpath('/Users/path_to_your_downloaded_and_extracted_codes'));
PC and Linux users need to pay attention to the path especially forward slash versus backward slash
An example tutorial using DeepTree algorithm for single-cell analysis can be found here
PCAPlot performs PCA of a matrix and plots multiple useful plots.
CCAPlot conduct Canonical correlation analysis of a datamatrix (usually Principal Component scores) and a metadata matrix (usually boolean and quantitative variables) and generate plots.
PCACCAPlot is similar to CCAPlot but performs a PCA for the datamatrix (which is usually a sample-by-gene matrix).
tsnePlot_old reduces the dimension of columns before Matlab 2018a
FilterTrend looks for genes highly correlated with a specified trend among a matrix in a rudimentary way. For example, for a matrix of 6 RNA-seq samples (Early Rep1, Early Rep2, Mid Rep1, Mid Rep2, Late Rep1, Late Rep2), setting Trend to [1 1 2 2 3 3] looks for genes that increase strictly linearly according to the sample state.
corrplot_dot is a third-party script modified by me to plot pairwise correlation values with scatterplot dots.
gplotmatrix dedicated for corrplot
gscatterTable plots a scatter plot with colors indicating classvar identities
GOTree plots a tree of GO terms specified. GOTreeColor is the colored version.
Gene10XCount plots the stacked bars of (fractions of) gene counts (usually a single-cell end-tagging UMI count matrix) at different abundance cutoffs. GeneCountSorted is a version that sorts bars. GeneFPKM is the equivalent version with cutoffs designed for SMART-seq (single-cell and bulk).
MetaCdfplot plots multiple cdf curves on the same figure.
donut is a third-party script that plots a donut plot, similar to a pie chart.
subplot1 is a third-party script that plots multiple panels.
venn is a third-party script to make Venn diagrams.
violin is a third-party script to make violin plots.
ValidizeNames sightly modifies a cell array so that it can be used for directly naming variables.
caseconvert is a third-party script to convert cases.
strcontain prints out the indices of elements that contains a substring.
strnotcontain does the opposite.
GetOrder compares two arrays with different orders and figures out how it was transformed from A to B. This is particularly useful when different metadata categories were stored in separate variables. The return of this function is a index array that can be used to reorder other companion arrays from the old order to the new order.
MatrixHighRanker takes a table of multiple columns of values writes the high-value (above cutoff) items into a text file named "outfile".
MatrixTopRanker takes a table of multiple columns of values writes the top rankers into a text file named "outfile".
MetaIntersect intersects the lists(columns) of string items stored in tableA and tableB in a pairwise fashion.
MetaHygecdf makes use of the output of MetaIntersect to calculate hypergeometric enrichment cdf between columns of tableA and tableB.
OneDim2TwoDim calculates the sum of Column C of each type of combinations of the elements in the first two columns (A & B) of a table.
Outersect outputs elements in A that are not in B.
TableHygecdf makes use of the intersect matrix (contingency table) to calculate hypergeometric enrichment cdf.
crosstab2 is a modified version of crosstab but with better output format.
tablecat concatenates two tables (columns of items) of string items stored in tableA and tableB
HeatMap2 plots a heatmap.
IntersectChecker compares multiple lists and summaries the intersection counts in a heatmap.
Mat2Colormap generates a heatmap color scheme.
redblue is a third-party script that generates a red-to-blue color scheme for color-blinded people.
rgb2map is a third-party script that converts RGB colors to indexed colormap colors.
scatplot is a third-party script to make scatter plots.
distinguishable_colors pick colors that are maximally perceptually distinct.
PlotSubsetFPKM generates a heatmap of a subset of genes from a gene-by-sample matrix.
subsetFPKMDimensionReduction wraps up PlotSubsetFPKM, PCAPlot and tsnePlot together.
SaveClusterColumnLabels write the ColumnLabels of a 1x1 clustergram into a file named as the clustergram.
SaveClusterRowLabels write the RowLabels of a 1x1 clustergram into a file named as the clustergram.
ImportBody and ImportBody2 read data in files and store them as variables. These primitive scripts are not recommended.
Mat2StrArray converts a matrix/vector nummat to a cell array of strings.
Table2DataMatrix converts a table into a datamatrix.
TableStr2Double converts a column of a table to the Double type.
mminfo is a third-party that reads the contents of the Matrix Market file 'filename' and extracts size and storage information.
mmread is a third-party script that reads Matrix Market file stores it into a matrix.
mmwrite is a third-party script that writes a matrix into a Matrix Market file.
msm_to_mm is a third-party script that writes a MATLAB Sparse Matrix to a Matrix Market file.
read10XCount imports 10X single-cell RNA-seq UMI counts in Matrix Market formats and converts it into a DataMatrix format.
write10XCount saves DataMatrix-format 10X single-cell RNA-seq UMI counts as MatrixMarket formats.
PlotBipar takes a matrix of connection values between Group A (row names) and Group B (column names) and plots a bipartite graph.
PlotNetwork plots a network graph based on the square adjacency matrix.
SaveCell write a nX1 cell array into a file named filename.
This repo demonstrates the possibility with these scripts to analyze genomics data including single-cell RNA-seq data. MATLAB is not open sourced. But it also doesn't have as much the pain as installing open-source python or R packages which have complicated compatibility issues. The repo here doesn't represent a final product but instead an initial effort to build a MATLAB community that has been underrepresented in the genomics field.