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Visualization settings

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jfnavarro edited this page Jun 15, 2020 · 7 revisions

The visualization settings panel defines how the data is plotted. This panel is only useful when visualizing genes and not spots colors (i.e. clusters).

Once genes are selected to be shown, the way the data is presented in the main view depends on the configuration defined in the visual settings.

  1. The Normalization controls allow to normalize the data
    • None: The data is not normalized
    • CPM: The expression of a gene in a spot is normalized by the total number of reads in that spot and multiplied by its mean expression value (reads)
    • REL: The expression of a gene in a spot is normalized by the total number of reads in that spot
    • Log scale: The expression (normalized or not) is in log2 space

Note that only the genes and spots that are shown and passing the filters will be used in the normalization.

  1. The Thresholds controls allow to define different filters on the spots and genes

    • Total Detected Genes (Per spot): Discards spots whose number of expressed genes is lower than the value defined
    • Minimum Transcripts: number of reads for a gene to be considered detected in a spot
    • Total Detected Spots (Per gene): Discards genes that are present in less spots than the number defined

  2. The Visualization mode controls allow to define different plotting modes

    • Default: the color of the spots will be a linear combination of the colors of each gene in that spot (genes that are selected and shown and pass the thresholds)
    • Dynamic range: similar to Default but the intensity of the color will correlate with the level of expression
    • Heatmap1: colors will be computed from a rainbow color map obtained using the spot with the lowest amount of expression and the spot with the highest amount of expression
    • Heatmap2: colors will be computed from a continuous lightness from black over fire colors to white obtained using the spot with the lowest amount of expression and the spot with the highest amount of expression

  3. The General settings controls allow to show/hide the legend (useful for some visualization modes), show/hide the image and define the size and intensity of the spots. The most important feature here is the "Show spots" checkbox. When this box is checked only the spots colors will be shown and when it is not checked the genes colors will be shown. With this checkbox we can easily switch between genes and spots colors.

Most of the visualization controls in this panel require to press the Update View button. The reason for doing so is to avoid un-necessary computation time.

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