2 Plot

2.1 Boxplot

Both wide matrix and long matrix data can be used to draw boxplot. In the demo1, we used the gene expression table in different samples with long matrix format and the metadata table of samples.

In the drawing parameters:

  • Specify the x-axis to display group information by selecting the option of conditions in the X-axis variable parameter;

  • Specify the y-axis to display the expression of genes in different samples by selecting the option of ENSG00000109689 in the Y-axis variable parameter;

  • Add lines of the paired samples in the two groups by selecting the option of individual in the Group variable for lining points parameter;

  • Use the color set “Set3” to color the boxes of two groups by selecting the option of Set3 in the Manual color vector (color set) parameter;

  • The Do statistics significane test for each group parameter is selected as yes so that a letter is added to the top of the box to show whether the gene is significantly different between the two groups.

2.2 Flower

In the demo1, paste two-column matrix with the sample information of genes.

In the drawing parameters:

  • Specify the column containing genes by selecting the option of Gene in the Column containing all items parameter;

  • Specify the column containing sample information by selecting the option of Sample in the Column containing all sets information parameter;

  • Change the label of the center circle which reflecting the number of common genes of all samples by inputting core in the textarea of Center circle label parameter.

2.3 Line plot

Both wide matrix and long matrix data can be used to draw line plot. In the demo1, we used the gene expression table in different samples with wide matrix format.

In the drawing parameters:

  • Use the color set “Set3” to color the lines of genes by selecting the option of Set3 in the Manual color vector (color set) parameter.

2.4 Pretty heatmap

In the demo1, we used the common gene expression profile which contains the expression of genes in different samples.

In the drawing parameters:

  • The Duplicate rownames parameter is selected as Automatically rename to deal with duplicate row names of data;

  • The Scale data parameter is selected as Raw to scale the rows of data for clustering and visualization;

  • Use the color set “Set3” to color the lines of genes by selecting the option of Set3 in the Manual color vector (color set) parameter.

2.5 Volcano plot

In the demo1, we used the different gene analysis result incluing all gene name, the mean of gene expression between the two groups, log2 fold change of gene expression in the two groups, statistical significance results, some interesting gene names, and the information whether the gene is different between the two groups.

In the drawing parameters:

  • Specify the name of the column whose value is log2 fold change of gene expression in the two groups by selecting the option of log2FoldChange in the Fold change column parameter;

  • Specify the name of the column whose value is statistical significance results by selecting the option of padj in the Statistical significance column parameter;

  • The Log10 transform significance value parameter is selected as Log 10 transform to transform log10 on the statistical significance results;

  • Specify the name of the column whose value is the information whether the gene is different in the two groups by selecting the option of Level in the Gene expression change status variable parameter;

  • After selecting the option of Level in the Gene expression change status variable parameter, the order of variables in the level can be set by selecting the order of the options of the Status variable order parameter;

  • Change the color transparency of points by inputting 0.4 in the textarea of Color transparency parameter;

  • Add the horizontal lines to show the significance threshold by inputting fdr in the textarea of Horizontal line positions parameter;

  • Add the horizontal and vertical lines to show the threshold of significance and log2 fold change by inputting 0.05,1 in the textarea of DE genes filtering threshold parameter. And if Gene expression change status variable parameter is empty, the parameter will automatically determine which genes are the different between the two groups based on the provided thresholds.

2.6 VennDiagram plot

In the demo1, paste two-column matrix with the sample information of genes.

In the drawing parameters:

  • Specify the column containing genes by selecting the option of Gene in the Column containing all items parameter;

  • Specify the column containing sample information by selecting the option of Sample in the Column containing all sets information parameter;

  • Samples of interest and order of presentation can be set by selecting Set1, Set2, Set3, Set4 (multiple options in order) of the Choose which sets to plot and their order parameter;

  • Change the label size by inputting 0.6 in the textarea of Label size parameter;

  • Change the blank range around the diagram by inputting 0.1 in the textarea of Margins parameter.

2.7 Enrichment plot

In the demo1, paste four-column matrix with the group information, GeneRatio, statistical significance results, the number of genes of GO terms, and the description of GO terms.

In the drawing parameters:

  • Specify the x-axis to display GeneRatio by selecting the option of geneRatio in the X-axis variable parameter;

  • Specify the y-axis to display the description of GO terms by selecting the option of Description in the Y-axis variable parameter;

  • Specify the color of points to display the statistical significance results by selecting the option of Qvalue in the Color variable parameter;

  • Neg log10 transform statistical significance results by selecting the option of Qvalue in the Neg log10 transform variable parameter;

  • Specify the size of points to display the number of genes of GO terms by selecting the option of Count in the Point size variable parameter;

  • Specify the shape of points to display the group information by selecting the option of SampleGroup in the Shape variable parameter.

2.8 Upsetview plot

Both wide matrix and long matrix with header data can be used to draw upsetview plot. In the demo1, paste wide matrix containing the name of movies and the style of movies.

In the drawing parameters:

  • Specify the threshold of intersections to plot by inputting 7 in the textarea of the Number of intersections to show parameter.

2.9 Scatter plot

In the demo1, paste four-column matrix with gene names, the sample information, gene expression, and gene percent.

  • Specify the x-axis to display gene by selecting the option of Gene in the X-axis variable parameter;

  • Specify the y-axis to display the sample information by selecting the option of Cluster in the Y-axis variable parameter;

  • Change the color of points to display the gene expression by selecting the option of Expr in the Color variable parameter;

  • Add the label of points to display the gene expression by selecting the option of Expr in the Point size variable parameter;

  • Change the size of points to display the gene percent by selecting the option of Percent in the Size variable parameter;

  • The Legend position parameter is selected as Top to put the legend above the graph.

2.10 Bar plot

Both wide matrix and long matrix data can be used to draw bar plot. In the demo1, we used the gene expression table in different samples with long matrix format.

  • Specify the x-axis to display sample information by selecting the option of ID in the X-axis variable parameter;

  • Specify the y-axis to display the expression of genes in different samples by selecting the option of Expression in the Y-axis variable parameter;

  • Change the color of points to display the gene expression by selecting the option of Gene in the Color variable parameter;

  • The Add text parameter is selected as True so that the texts are added to bars to display the gene expressions;

  • Change the font size by inputting 10 in the textarea of Base font size parameter;

  • Use the color set “Set3” to color the bars by selecting the option of Set3 in the Manual color vector (color set) parameter.

2.11 Histogram

Both wide matrix and long matrix data can be used to draw histogram. In the demo1, we used a data which is the weight in different genders with long matrix format.

In the drawing parameters:

  • Specify the x-axis to display weight by selecting the option of weight in the X-axis variable parameter;

  • Use the gender as group information by selecting the option of sex in the Group variable parameter;

  • Specify the y-axis to display the density of weight by selecting the option of Density in the Y-axis variable parameter;

  • The graph is composed of histogram and density curve by selecting the option of Line and Histogram in the Plot type parameter;

  • Fill areas parameter is selecting as True to fill the plot with colors;

  • Vline at mean value parameter is selecting as True to add vertical lines for each group.

2.12 EulerDiagrams plot

In the demo1, paste two-column matrix with the sample information of genes.

In the drawing parameters:

  • The Specified input format parameter need to be selected as Items due to the need to count the number of genes in different sets;

  • Specify the column containing genes by selecting the option of Gene in the Column containing all items parameter;

  • Specify the column containing sample information by selecting the option of Sample in the Column containing all sets information parameter;

  • Set Plot type parameter to Counts to add the number of genes in different sets;

  • Set Plot shape parameter to Circle to make the graph corresponding to all groups circular;

  • Change the font size for numbers by inputting 1 in the textarea of Font size for numbers parameter;

  • Change the font size for labels by inputting 1 in the textarea of Font size for labels parameter;

  • Set Line type parameter to Soild to make the edge of the graph the solid lines;

  • Change the color transparency of points by inputting 0.6 in the textarea of Color transparency parameter.

2.13 Non-classical venn

In the demo1, paste two-column matrix with the sample information of genes.

In the drawing parameters:

  • Specify the column containing genes by selecting the option of Gene in the Column containing all items parameter;

  • Specify the column containing sample information by selecting the option of Sample in the Column containing all sets information parameter;

  • Specify the interest samples to display by selecting the option of Set1, Set2, Set3 in the Select sets to show parameter;

  • The Do weighted parameter is selected as No so that do not calculate the weight of the data;

  • The Venn type parameter is selected as Triangles so that each set is displayed as a triangle and combined into a triangle;

  • The Show the set label parameter is selected as True so that each set is displayed as a triangle and combines into a triangle;

  • Add the sample name on the graph by selecting True in the Show the set label parameter;

  • Fill the sets with colors by selecting True in the Fill set parameter;

  • Add the sample boundaries on the graph by selecting True in the Show boundaries of the Sets parameter;

  • Add the elements information of different sets on the graph by selecting Elements in the FaceText parameter.