plot_pathway_heatmap: Plot pathway heatmap
In jacobheng/cellwrangler: Supplemental toolkit for single-cell RNAseq analysis

Description Usage Arguments Value Examples

plot_pathway_heatmap() plots the results of output from the fgsea() function.

plot_pathway_heatmap(path_table = NULL, path_res_df,
  color_scale = c("blue", "lightyellow", "red"), cluster_row = T,
  cluster_col = T, mark_sig = T, sig_para = "pval",
  sigCutoff = 0.05, clustering_distance_rows = "euclidean",
  clustering_method_rows = "complete",
  clustering_distance_cols = "euclidean",
  clustering_method_cols = "complete", flip_axes = F,
  square_tiles = T)

`path_table`	a dataframe of values
`path_res_df`	dataframe should contain columns "CellType", "pathway", "NES";can be output from the fgsea() function
`color_scale`	vector of colors to use for color scale; different options for color_scale_type requires different number of colors - "diverge" (3 colors), "seq" (2 colors), "rescale" (3 colors)
`mark_sig`	logical; whether to mark statistically significant results with a "*".
`sig_para`	parameter for statistical significance.
`sigCutoff`	cutoff for statistical significance.
`clustering_distance_rows`	distance measure used in clustering rows. Possible values are "correlation", "euclidean", "maximum", "manhattan", "canberra", "binary", or "minkowski" (defined in dist() function.)
`clustering_method_rows`	clustering method used for rows. Accepts the same values as hclust: "ward.D", "ward.D2", "single", "complete", "average" (=UPGMA), "mcquitty" (=WPGMA), "median" (=WPGMC) or "centroid" (=UPGMC).
`clustering_distance_cols`	distance measure used in clustering columns. Possible values are the same as clustering_distance_rows.
`clustering_method_cols`	clustering method used for columns. Accepts the same values as clustering_method_rows.
`flip_axes`	logical; if x- and y-axes should be flipped
`square_tiles`	logical; if tiles should made into squares
`cluster_rows`	logical; if rows should be clustered
`cluster_cols`	logical; if columns should be clustered