The function is intended to be called within the custom_heatmap_wrapper

The function creates a segmented heatmap where rows are samples/patients and columns are genes. The heatmap is column segmented based on the number of differential expression analyses contained within it. A log2foldChange histogram is attached to the bottom of the heatmap to indicate significance of the genes being visualized.

The column/segment legend is given at the bottom of the heatmap with the number of genes in each group being also provided.

The gradient legend of the values within the heatmap is given on the right hand side.

The heatmap is saved in both png and svg format.

plot_custom_DE_heatmap(
  heat_mat,
  col_split,
  row_splits,
  l2fc_col,
  log_transform,
  color_vect,
  legend_value = "counts",
  plot_file_name = "custom_heatmap",
  custom_width = 15,
  custom_height = 5,
  do_SVG = TRUE
)

Arguments

heat_mat

The main count matrix of the heatmap

col_split

The named vector used to split the columns into it's segments

row_splits

The named vector used to split the rows into the two groups

l2fc_col

The log2foldchange vector used to create the histogram

log_transform

boolean indicating if the results were log transformed or not

color_vect

A vector for the colors to be used in the heatmap

legend_value

string indicating the type of value used (counts for RNAseq, intensity value for microarray)

plot_file_name

The name given to the saved heatmap

custom_width

The width of the heatmap

custom_height

The height of the heatmap

do_SVG

Boolean to check if the SVG file should be created or not

Value

none or heatmap plot

Examples

TS_object<-create_example_object_for_R()
TS_object <- normalize_timeSeries_with_deseq2(time_object=TS_object)
#> converting counts to integer mode
#Perform conditional differential gene expression analysis
TS_object<-conditional_DE_wrapper(TS_object,vignette_run=TRUE)
heat_dta<-create_conditional_heatmap_matrix(TS_object)
heat_dta<-prepare_heat_data(heat_dta,log_transform=TRUE)

log_l2fc<-log_transform_l2fc_vect(heat_dta[['l2fc_vector']])

heat_plot<- plot_custom_DE_heatmap(heat_dta[['heat_matrix']],heat_dta[['region_split']],
                                   heat_dta[['group_split']],log_l2fc,log_transform = TRUE,
                                   legend_value='counts', plot_file_name = NULL,
                                   do_SVG=FALSE)
#> Error in plot_custom_DE_heatmap(heat_dta[["heat_matrix"]], heat_dta[["region_split"]],     heat_dta[["group_split"]], log_l2fc, log_transform = TRUE,     legend_value = "counts", plot_file_name = NULL, do_SVG = FALSE): argument "color_vect" is missing, with no default