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Functions renamed in hyperSpec #21

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Functions renamed in hyperSpec #21

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d39cefa
Update chondro.R
GegznaV Aug 7, 2022
490667f
Update hySpc-chondro.Rmd
GegznaV Aug 7, 2022
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4 changes: 2 additions & 2 deletions R/chondro.R
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Original file line number Diff line number Diff line change
Expand Up @@ -28,13 +28,13 @@
#' chondro <- chondro - quantile(chondro, 0.05)
#'
#' cols <- c("dark blue", "orange", "#C02020")
#' plotmap(chondro, clusters ~ x * y, col.regions = cols)
#' plot_map(chondro, clusters ~ x * y, col.regions = cols)
#'
#' cluster.means <- aggregate(chondro, chondro$clusters, mean_pm_sd)
#' plot(cluster.means, stacked = ".aggregate", fill = ".aggregate", col = cols)
#'
#' ## plot nucleic acid bands
#' plotmap(chondro[, , c(728, 782, 1098, 1240, 1482, 1577)],
#' plot_map(chondro[, , c(728, 782, 1098, 1240, 1482, 1577)],
#' col.regions = colorRampPalette(c("white", "gold", "dark green"), space = "Lab")(20)
#' )
NULL
28 changes: 14 additions & 14 deletions vignettes/hySpc-chondro.Rmd
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Expand Up @@ -225,10 +225,10 @@ CAPTION <- "The sum intensity of the raw spectra."
seq_palette <- colorRampPalette(c("white", "dark green"), space = "Lab")
```
```{r rawmap, fig.cap=CAPTION}
plotmap(chondro, func.args = list(na.rm = TRUE), col.regions = seq_palette(20))
plot_map(chondro, func.args = list(na.rm = TRUE), col.regions = seq_palette(20))
```

Function `plotmap()`{.r} squeezes all spectral intensities into a summary characteristic for the whole spectrum.
Function `plot_map()`{.r} squeezes all spectral intensities into a summary characteristic for the whole spectrum.
This function defaults to the `mean()`{.r}.
Further arguments that should be handed to this function can be given in list `func.args`{.r}.
As the raw data contains `NA`{.r}s due to deleting cosmic ray spikes, this argument is needed here.
Expand All @@ -249,7 +249,7 @@ complete (square) is retained but only few positions on this grid.

Occasionally, numeric or rounding errors will lead to seemingly irregular spacing of the data
points.
This is most obvious in false-colour maps of the sample (fig. \@ref(fig:rawmap), as `plotmap`{.r} by default uses `panel.levelplot.raster`{.r}, which assumes a regular grid is underlying the data.
This is most obvious in false-colour maps of the sample (fig. \@ref(fig:rawmap), as `plot_map`{.r} by default uses `panel.levelplot.raster`{.r}, which assumes a regular grid is underlying the data.
The symptoms are warnings "`'x' values are not equispaced; output may be wrong`" and white stripes in the false colour map (fig. \@ref(fig:irregular-a)), which occur even thought the points are almost at their correct place (fig. \@ref(fig:irregular-b)).


Expand All @@ -269,12 +269,12 @@ Rounding erros in the point coordinates of lateral measurement grid:
```

```{r irregular-a, fig.cap=CAPTION}
plotmap(chondro, col.regions = seq_palette(20))
plot_map(chondro, col.regions = seq_palette(20))
```

```{r irregular-a-sub, include=FALSE}
# For subplot A
irregular_grid_a <- as.ggplot(plotmap(chondro, col.regions = seq_palette(20)))
irregular_grid_a <- as.ggplot(plot_map(chondro, col.regions = seq_palette(20)))
```
<!-- --------------------------------------------------------------------- -->

Expand All @@ -289,7 +289,7 @@ Rounding erros in the point coordinates of lateral measurement grid:

```{r irregular-b, fig.cap=CAPTION}
library("latticeExtra")
plotmap(chondro,
plot_map(chondro,
col.regions = seq_palette(20), panel = panel.levelplot.points,
col = NA, pch = 22, cex = 1.9
)
Expand All @@ -298,7 +298,7 @@ plotmap(chondro,
```{r irregular-b-sub, include=FALSE}
# For subplot B
irregular_grid_b <- as.ggplot(
plotmap(chondro, col.regions = seq_palette(20), panel = panel.levelplot.points,
plot_map(chondro, col.regions = seq_palette(20), panel = panel.levelplot.points,
col = NA, pch = 22, cex = 1.9)
)
```
Expand All @@ -324,12 +324,12 @@ Rounding erros in the point coordinates of lateral measurement grid:
```

```{r irregular-c, fig.cap=CAPTION}
plotmap(chondro, col.regions = seq_palette(20))
plot_map(chondro, col.regions = seq_palette(20))
```

```{r irregular-c-sub, include=FALSE}
# For subplot C
irregular_grid_c <- as.ggplot(plotmap(chondro, col.regions = seq_palette(20)))
irregular_grid_c <- as.ggplot(plot_map(chondro, col.regions = seq_palette(20)))
```
<!-- --------------------------------------------------------------------- -->

Expand Down Expand Up @@ -606,7 +606,7 @@ CAPTION <- "Hierarchical cluster analysis: the cluster map for $k=3$ clusters. "
```

```{r clustmap, fig.cap=CAPTION}
print(plotmap(chondro, clusters ~ x * y, col.regions = cols))
print(plot_map(chondro, clusters ~ x * y, col.regions = cols))
```

The cluster membership can also be marked in the dendrogram:
Expand Down Expand Up @@ -658,7 +658,7 @@ CAPTION <- "False color map of DNA. "

```{r DNA, fig.cap=CAPTION}
DNAcols <- colorRampPalette(c("white", "gold", "dark green"), space = "Lab")(20)
plotmap(chondro[, , c(728, 782, 1098, 1240, 1482, 1577)],
plot_map(chondro[, , c(728, 782, 1098, 1240, 1482, 1577)],
col.regions = DNAcols
)
```
Expand All @@ -681,7 +681,7 @@ CAPTION <- "False colour map of the DNA band intensities: smoothed DNA abundance
```

```{r DNAsm, fig.cap=CAPTION}
plotmap(chondro[, , c(728, 782, 1098, 1240, 1482, 1577)],
plot_map(chondro[, , c(728, 782, 1098, 1240, 1482, 1577)],
col.regions = DNAcols,
panel = panel.2dsmoother, args = list(span = 0.05)
)
Expand All @@ -701,7 +701,7 @@ CAPTION <- 'Two-dimesional (2D) "constant" interpolation with missing values: om
```

```{r DNAmissing, fig.cap=CAPTION}
plotmap(tmp, col.regions = DNAcols)
plot_map(tmp, col.regions = DNAcols)
```


Expand All @@ -711,7 +711,7 @@ CAPTION <- 'Two-dimesional (2D) "constant" interpolation with missing values: De
```

```{r DNAvoronoi, fig.cap=CAPTION}
plotmap(tmp,
plot_map(tmp,
col.regions = DNAcols,
panel = panel.voronoi, pch = 19, col = "black", cex = 0.1
)
Expand Down