hicPCA: The A/B compartments of the X chromosome is not properly recognized

[lscnsdad]

Hello, I have a problem that is difficult to solve：

My command is as follows：

hicCorrectMatrix correct -m hn_matrix_150kb.h5 \
                         --filterThreshold -1.5 3.6 \
                         -o hn_corrected_150kb.h5

hicPlotMatrix -m hn_corrected_150kb.h5 -o hn_corrected_150.png --log1p

hicPCA --matrix hn_corrected_150kb.h5 \
       --pearsonMatrix hn_pearson_150kb.h5 \
       --outputFileName pca1_r.bw pca2_r.bw \
       --format bigwig --whichEigenvectors 1 2

hicPlotMatrix \
  -m hn_pearson_150kb.h5 \
  --outFileName hn_improved_matrix_all2.png \
  --title "Hi-C Matrix with PC1" \
  --dpi 150 \
  --fontsize 10 \
  --rotationX 45 \
  --rotationY 0 \
  --bigwig pca1_r.bw \
  --vMinBigwig -0.1 \
  --vMaxBigwig 0.1 \
  --increaseFigureHeight 0.8

PCA1：

PCA2：