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Plotting heatmap by binary values
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12 months ago
F ♦ 3.4k
Iran

Hi,

I have a matrix, rows are genes and columns are DAVID GO terms + logFC of genes in a separate columns

I want to plot a heat by considering logFC of genes, but I don't know how

> head(heat)
      focal adhesion cell-cell adherens junction cadherin binding involved in cell-cell adhesion muscle contraction
MYL9               0                           0                                               0                  1
ACTB               1                           0                                               0                  0
ACTA2              0                           0                                               0                  1
ACTG2              0                           0                                               0                  1
PFN1               1                           1                                               1                  0
HSPB1              1                           0                                               0                  0
      fibronectin binding myelin sheath extracellular matrix integrin binding cytoskeleton     logFC
MYL9                    0             0                    0                0            0 -1.579165
ACTB                    0             1                    0                0            1 -1.482387
ACTA2                   0             0                    0                0            0 -2.379757
ACTG2                   0             0                    0                0            0 -2.144757
PFN1                    0             0                    0                0            1 -1.158010
HSPB1                   0             0                    1                0            1 -1.172407
>

Any feasible way to have a clear heatmap?

r heatmap • 169 views
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The heatmap is long because you have too many GO terms. If you don't have too many genes, you could rotate the table. Otherwise, take advantage of the ontology structure to group terms or plot only those most relevant to the biology under consideration.

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What have you tried?

Also, Jean-Karim's comment suggests you probably had something about a heatmap taking too long. Did you remove any such content in your edit?

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