Re-order Correlation heatmap¶
usage: plot_corr_reorder.py [-h] -f INPUT -n REORDER_NAMES [-s SEP]
[--skiprows SKIPROWS] [-o OUTPUT]
optional arguments:
-h, --help show this help message and exit
-f INPUT, --input INPUT
correlation matrix with index and header (default:
None)
-n REORDER_NAMES, --reorder_names REORDER_NAMES
two columns showing old names and new names (default:
None)
-s SEP, --sep SEP this program can infer separator automatically, but it
may fail. Use auto if the input tables contain
different separators. (default: auto)
--skiprows SKIPROWS Pandas read_csv parameter to skip first N rows
(default: 0)
-o OUTPUT, --output OUTPUT
output file name (default: yli11_2020-04-07)
Summary¶
Plot correlation heatmap given correlation matrix.
One usage: When using bw corr, the result figure can look bad because of large number of files (>50). In this case, you want to plot your own figures using their output.
This program allows you to rename and re-order columns and rows.
Note this program requires the matrix, which is plotCorrelation.tab
and a name mapping file (old name and new name). Old names should match the column names in plotCorrelation.tab
, which is the file names if you start with bw_corr.py
.
Input¶
A correlation matrix with index name and column names.
A new names tsv file (e.g., row_name_mapping.txt), 2 columns: old name and new name
SE_H1.bw SE_H1
PE_CLONE85.bw PE_CLONE85
SE_CLONE85.bw SE_CLONE85
PE_H2.bw PE_H2
SE_A17.bw SE_A17
PE_A16.bw PE_A16
SE_A16.bw SE_A16
SE_H2.bw SE_H2
K562.bw K562
PE_H1.bw PE_H1
PE_A17.bw PE_A17
H2_WT.bw H2_WT
H2_195C_G.bw H2_195C_G
Output¶
Usage¶
Go to your data directory and type the following.
Step 0: Load python version 2.7.13.
hpcf_interactive
module load python/2.7.13
plot_corr_reorder.py -f plotCorrelation.tab --skiprows 1 -s "\t" -o test.png -n row_name_mapping.txt
plotCorrelation.tab
is an output from bw corr, the first line is notes, so we skip the first row when read the file using --skiprows 1
.