What is a dot plot and how do you read it?

What is a dot plot and how do you read it?

In summary, a Dot Plot is a graph for displaying the distribution of quantitative variable where each dot represents a value. For whole numbers, if a value occurs more than once, the dots are placed one above the other so that the height of the column of dots represents the frequency for that value.

What do the diagonals in the dot plot represent?

The main diagonal represents the sequence’s alignment with itself; lines off the main diagonal represent similar or repetitive patterns within the sequence.

What is Seurat clustering?

Graph-based clustering is performed using the Seurat function FindClusters, which first constructs a KNN graph using the Euclidean distance in PCA space, and then refines the edge weights between any two cells based on the shared overlap in their local neighborhoods (Jaccards distance).

What does a dot plot tell you?

A dot plot is similar to a histogram in that it displays the number of data points that fall into each category or value on the axis, thus showing the distribution of a set of data.

How do you describe a dot plot distribution?

Dot plots (or line plots) show clusters, peaks, and gaps in a data set. You can also use a dot plot to identify the shape of a distribution. All the dots are about the same height. A distribution is skewed left when most of the data are on the right and skewed right when most of the data are on the left.

What do you mean by window size and threshold of the dot plot?

Each axis of a dotplot represents the linear arrangement of one sequence being compared. A short segment of one sequence (also called window size) is compared with all possible segments of the same length in the second sequence. This generates a matrix of several alignments between the two sequences.

What is the difference between a dot plot and a scatter plot?

A dot plot is just a bar chart that uses dots to represent individual quanta. A scatter plot puts a point representing a single realization of a tuple of data. For example, if you measured people’s height and weight, you could create a scatter plot where one axis represented height and one represented weight.

When to use the dotplot function in Seurat V3?

I want to use the DotPlot function from Seurat v3 to visualise the expression of some genes across clusters. However when the expression of a gene is zero or very low, the dot size is so small that it is not clearly visible when printed on paper.

How to increase the minimum dot size in Seurat?

However when the expression of a gene is zero or very low, the dot size is so small that it is not clearly visible when printed on paper. Please is there a possibility to increase the minimum dot size in the DotPlot function to make the dot sizes more visible when printed?

How is average expression different from dot plot?

The calculated average expression value is different from dot plot and violin plot. Also the two plots differ in apparent average expression values (In violin plot, almost no cell crosses 3.5 value although the calculated average value is around 3.5). Same assay was used for all these operations.

What’s the difference between dot plot and violin plot?

Same assay was used for all these operations. In dot plot, the difference in average expression between two groups appears exaggerated after considering violin plot and calculated values. Kindly help me to understand these apparent discrepancies. I think DotPlot using scaled (z-score) of data used in VlnPlot: