Visualize pairwise log odds ratios (LOR) for data that are available in both cases and controls

Visualize pairwise log odds ratios (LOR) for data that are available in both cases and controls

Usage

plot_logORmat(data_nplcm, pathogen_display, BrS_slice = 1, logOR_rounding = 2)

Arguments

data_nplcm

See assign_model().

pathogen_display

The pathogen vector in desired order for display. It can be of larger length than that of pathogen_BrS.

BrS_slice

Default is 1 - the set of BrS data to visualize.

logOR_rounding

Rounding number of the log odds ratio. Default is 2.

Value

Figure of LOR matrix and relevant s.e. and significance information.

Details

plot_logORmat visualizes a matrix of pairwise log odds ratios (LOR) for cases (upper) and controls (lower). LOR is at the top of the cell. Below it, its standard error is in smaller type, using the same color as the LOR. Then the estimate is divided by its standard error. We put the actual value when the Z-statistics has an absolute value greater than $2$; a plus (red) or minus (blue) if between $1$ and $2$; blank otherwise.

See also

Other exploratory data analysis functions: get_top_pattern(), show_individual(), summarize_BrS(), summarize_SS(), visualize_season()

Examples

data(data_nplcm_noreg)
plot_logORmat(data_nplcm_noreg,names(data_nplcm_noreg$Mobs$MBS[[1]]))
#> == Visualizing pairwise log odds ratios for bronze-standard data set:  1 :  MBS1 . ==