View source: R/plot_variant_influences.R
plot_variant_influences | R Documentation |
This function plots the the cape coefficients between pairs of markers as a heat map. The interactions are shown in the main part of the heatmap while the main effects are shown on the right hand side. Directed interactions are read from the y axis to the x axis. For example an interaction from marker1 to marker2 will be shown in the row corresponding to marker1 and the column corresponding to marker2. Similarly, if marker1 has a main effect on any traits, these will be shown in the row for marker1 and the trait columns.
plot_variant_influences( data_obj, p_or_q = 0.05, min_std_effect = 0, plot_all_vals = FALSE, standardize = FALSE, color_scheme = c("DO/CC", "other"), pos_col = "brown", neg_col = "blue", not_tested_col = "lightgray", show_marker_labels = FALSE, show_chr = TRUE, label_chr = TRUE, show_alleles = TRUE, scale_effects = c("log10", "sqrt", "none"), pheno_width = NULL, covar_width = NULL, covar_labels = NULL, phenotype_labels = NULL, show_not_tested = TRUE )
data_obj |
a |
p_or_q |
A threshold indicating the maximum p value (or q value if FDR was used) of significant interactions and main effects |
min_std_effect |
An optional filter. The plot will exclude all pairs with standardized effects below the number set here. |
plot_all_vals |
If TRUE will plot all values regardless of significant |
standardize |
Whether to plot effect sizes (FALSE) or standardized effect sizes (TRUE) |
color_scheme |
A character value of either "DO/CC" or other indicating the color scheme of main effects. If "DO/CC" allele effects can be plotted with the DO/CC colors. |
pos_col |
The color to use for positive main effects and interactions
must be one of "green", "purple", "red", "orange", "blue", "brown", "yellow", "gray"
see |
neg_col |
The color to use for negative main effects and interactions takes the same values as pos_col. |
not_tested_col |
The color to use for marker pairs not tested. Takes the same values as pos_col and neg_col |
show_marker_labels |
Whether to write the marker labels on the plot |
show_chr |
Whether to show chromosome boundaries |
label_chr |
Whether to label chromosomes if plotted |
show_alleles |
If TRUE, the allele of each marker is indicated by color. |
scale_effects |
One of "log10", "sqrt", "none." If some effects are very large, scaling them can help show contrasts between smaller values. The default is no scaling. |
pheno_width |
Each marker and trait gets one column in the matrix. If there are many markers, this makes the effects on the traits difficult to see. pheno_width increases the number of columns given to the phenotypes. For example, if pheno_width = 11, the phenotypes will be shown 11 times wider than individual markers. |
covar_width |
See pheno_width. This is the same effect for covariates. |
covar_labels |
Labels for covariates if different from those stored in the data object. |
phenotype_labels |
Labels for traits if different from those stored in the data object |
show_not_tested |
Whether to color the marker pairs that were not tested. If FALSE, they will not be colored in. |
This function invisibly returns the variant influences matrix. shown in the heat map.
## Not run: plot_variant_influences(data_obj) ## End(Not run)
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