There is a discrepancy between the values plotted on the heatmap and in the infercnv_obj@expr.data slot

When running plot_cnv(), there is an option called x.range that limits the min/max values that are plotted to avoid outliers skewing the color breaks and toning down all color intensities. By default, it is set to "auto", which sets the min/max limits to respectively the 0.01 and 0.99 quantiles of the values in infercnv_obj@expr.matrix, setting the outliers to those limit values and effectively reducing the range() of the values in the .txt files.