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rp-valuecomplexheatmap

Values for asterisks incorrectly placed on heat map

I want to put asterisks in the heat map for P-values < 0.05. I have a separate spreadsheet with the P-values that I read into R and subsequently the heat map, however, the function i'm using doesn't seem to place the asterisks in the right cells. In the Figure below, for example, there are no P-values attached to the rho = 0 cells, and yet there are asterisks placed there.

image

Spreadsheet is shown below. For all P-values that are NA, I put in "1" to avoid an error. If there's a better way to do this on top of fixing the placements of the asterisks, please let me know. image

The code that i'm using is as follows:

library(circlize)
library(ComplexHeatmap)
library(Hmisc)

sx_syn_p <- read.csv('spear_synx1_p.csv', header=TRUE)

Shime1x_syn_spearman1 <- Heatmap(sx_syn, circlize::colorRamp2(c(-1, -0.5, 0, 0.5, 1), 
                                                                        c('#d7191c', '#fdae61',
                                                                          '#FFFFFF', '#abd9e9', 
                                                                          '#2c7bb6')),
                                column_names_gp=grid::gpar(fontsize=20,
                                                           col=c(rep('#4daf4a', 8), rep('#984ea3',7))),
                                row_names_gp=grid::gpar(fontsize=20, 
                                                        col=c(rep('#4daf4a', 8), rep('#984ea3',7))),
                                heatmap_legend_param=list(title="Spearman's rho", 
                                                          direction='horizontal',
                                                          at = c(-1, -0.5, 0, 0.5, 1)),
                   cell_fun = function(j, i, x, y, w, h, fill){
                     if(sx_syn_p[i, j] < 0.05) {
                       grid.text('*', x, y)
                     }
                   })
sx_syn1_spear <- draw(Shime1x_syn_spearman1, heatmap_legend_side='top')

I thought the function inputs asterisks based on P < 0.05 from the spreadsheet, but the inputs does not seem to be placed correctly.

Solution

  • I managed to fix this by removing the first column of labels in the spreadsheet and re-running the code. I think that converting the data frame as a matrix would give further assurance per this example. The issue with my code was that the order of sx_syn was not the same as sx_syn_p.