plot_marginal_activation: Marginal activation plot
In greenelab/ADAGEpath: ADAGE-based Signature Analysis
View source: R/marginal_activity.R
plot_marginal_activation R Documentation
Marginal activation plot
Description
Plots the activation significance of the marginal effects of signatures.
The value of the heatmap represents -log10 transformed adjusted p value from
the activation test when the effect of the column signature is removed from
the row signature. Values in the diagonal of the heatmap are the activation
significance of signatures themselves.
Usage
plot_marginal_activation(marginal_limma_result, signature_order = NULL,
sig_cutoff = 0.05)
Arguments
marginal_limma_result
a data.frame that stores the limma result table
returned by the build_limma() function when used on marginal activity.
It's rownames is in the format of "signature1-signature2".
signature_order
a vector of signature names, the order of signatures
in this vector will be used to order signatures in the plot. If NULL,
signatures will be ordered alphabatically. (default: NULL)
sig_cutoff
a numeric value used as the significance cutoff.
Significance values below the cutoff will be crossed out in the plot.
(default: 0.05)
greenelab/ADAGEpath documentation built on May 25, 2022, 7:11 a.m.
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View source: R/marginal_activity.R
| plot_marginal_activation | R Documentation |
Marginal activation plot
Description
Plots the activation significance of the marginal effects of signatures. The value of the heatmap represents -log10 transformed adjusted p value from the activation test when the effect of the column signature is removed from the row signature. Values in the diagonal of the heatmap are the activation significance of signatures themselves.
Usage
plot_marginal_activation(marginal_limma_result, signature_order = NULL, sig_cutoff = 0.05)
Arguments
marginal_limma_result |
a data.frame that stores the limma result table returned by the build_limma() function when used on marginal activity. It's rownames is in the format of "signature1-signature2". |
signature_order |
a vector of signature names, the order of signatures in this vector will be used to order signatures in the plot. If NULL, signatures will be ordered alphabatically. (default: NULL) |
sig_cutoff |
a numeric value used as the significance cutoff. Significance values below the cutoff will be crossed out in the plot. (default: 0.05) |
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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