create_corr_heatmap() calculates the correlation matrix of the input dataset.
It creates a heatmap of the correlation matrix. It also filters the protein
pairs with correlation values above the threshold and returns them in a tibble.
Usage
create_corr_heatmap(
x,
y = NULL,
use = "pairwise.complete.obs",
method = "pearson",
threshold = 0.8,
cluster_rows = TRUE,
cluster_cols = TRUE,
show_heatmap = TRUE
)Arguments
- x
A numeric vector, matrix or data frame.
- y
A numeric vector, matrix or data frame with compatible dimensions with
x. Default is NULL.- use
A character string. The method to use for computing correlations. Default is "pairwise.complete.obs".
- method
A character string. The correlation method to use. Default is "pearson".
- threshold
The reporting protein-protein correlation threshold. Default is 0.8.
- cluster_rows
Whether to cluster the rows. Default is TRUE.
- cluster_cols
Whether to cluster the columns. Default is TRUE.
- show_heatmap
Whether to show the heatmap. Default is TRUE.
Value
A list containing the following elements:
cor_matrix: A matrix of protein-protein correlations.
cor_results: A tibble with the filtered protein pairs and their correlation values.
cor_plot: A heatmap of protein-protein correlations.
Examples
# Prepare data
df <- example_data |>
dplyr::select(DAid, Assay, NPX) |>
tidyr::pivot_wider(names_from = "Assay", values_from = "NPX") |>
dplyr::select(-DAid)
# Correlate proteins
results <- create_corr_heatmap(df, threshold = 0.7)
# Print results
results$cor_plot # Heatmap of protein-protein correlations
results$cor_matrix[1:5, 1:5] # Subset of the correlation matrix
#> AARSD1 ABL1 ACAA1 ACAN ACE2
#> AARSD1 1.00 0.47 0.19 -0.06 0.04
#> ABL1 0.47 1.00 0.46 -0.01 0.13
#> ACAA1 0.19 0.46 1.00 0.03 0.32
#> ACAN -0.06 -0.01 0.03 1.00 0.07
#> ACE2 0.04 0.13 0.32 0.07 1.00
results$cor_results # Filtered protein pairs exceeding correlation threshold
#> Protein1 Protein2 Correlation
#> 1 ATP5IF1 AIFM1 0.76
#> 2 AXIN1 ARHGEF12 0.76
#> 3 AIFM1 ATP5IF1 0.76
#> 4 ARHGEF12 AXIN1 0.76
#> 5 ARHGEF12 AIFM1 0.71
#> 6 AIFM1 ARHGEF12 0.71