Interpreting the figure
The resulting example.pdf file from the quick start should look like the following figure.
The rows of the both heat maps in the visualization are cells. The heat maps are separated horizontally between reference and non-reference cells (or observations) with a color bar indicating different contig regions (by color change). The very top heat map is comprised of reference observations ordered by in the order given by the --ref parameter. The lower heat map is contains non-reference cells (observations) ordered using hierarchical clustering (euclidean distance, average linkage).
The columns of the figure are genes. Genes are separated with black vertical lines as contigs/chromosomes. The horizontal color bar between the two heat maps also indicates contigs/chromosomes by color change. Contigs/chromosomes are defined in and ordered by the Genomic Position File.
To create the measurements input values are converted to log2((TPM/10)+1) transformed and filtered requiring a minimum average per gene. The remaining raw gene values are then centered and thresholded to reduce outliers. Cells are then ordered by contig and smoothing is performed using a moving average using the cell's centered expression along the genomic coordinates. Ends of the contigs are removed (set to 0; due to being unreliable). This smoothed gene expression is then averaged in the reference observations and removed from the non-reference cells (if no reference is given a global average is used). If a gene measurement is too close to the average, it is set to zero (and is considered noise or existing genomic structure).
Both heat maps can be used in interpretation and focus on different information.
Interpreting Observations
The lower heat map in the example.pdf (shown above) uncovers patterns of expression consistent with genomic order that are not in the reference. One can infer these increases and decreased in expression to be a result of copy number variation. In this example we see deletions of Chr1p and Chr19q which are characteristic of oligodendroglioma.
Interpreting References
The upper heat map in the example.pdf (shown above) shows no real pattern and is primarily white. This tells us that the cells (reference and observation) have been treated in such a way the signal in the references has been removed and is not driving patterns in the observations. If columns of variation in the observations also appeared in the references, one could not be sure that signal is specific to the phenotype of the observation cells. Refer to Analysis with Controls for a walkthrough on how to use reference (control) samples.